Contacts of the helix formed by residues 94 - 117 (chain G) in PDB entry 2I2X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 94 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLN* 3.2 31.0 + - - +
91G MET 3.2 7.4 - - - +
92G SER 3.1 0.4 - - - -
93G ASN* 1.3 85.1 - - - +
95G PRO* 1.3 69.9 - - - +
96G SER* 3.1 4.0 - - - +
97G TRP* 2.8 51.8 + - + +
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Residues in contact with PRO 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G MET 4.1 5.4 - - - +
92G SER 3.8 5.8 - - - +
93G ASN 3.6 8.3 - - - +
94G ASN* 1.3 85.4 - - - +
96G SER* 1.3 62.4 + - - +
98G GLY* 3.0 6.1 + - - -
99G ALA* 3.0 20.3 + - - +
145G VAL* 3.8 20.9 - - + +
148G GLU* 3.8 27.6 - - + +
149G ALA* 4.1 14.9 - - - +
152G GLN* 3.9 26.9 - - + +
153G CYS* 5.0 1.0 - - - -
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Residues in contact with SER 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LYS* 5.1 2.6 + - - +
94G ASN* 4.3 2.8 + - - +
95G PRO* 1.3 79.4 - - - +
97G TRP* 1.3 71.9 + - - +
99G ALA* 3.7 2.8 - - - +
100G GLU* 2.9 48.6 + - - +
152G GLN* 3.9 16.1 + - - -
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Residues in contact with TRP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLY 4.6 1.3 - - - -
53G ALA 4.0 16.2 - - - -
54G SER* 4.4 1.8 - - - -
55G LYS* 3.6 65.3 - - + +
58G LEU* 4.2 13.7 - - + -
90G GLN* 3.8 42.6 - - + +
91G MET* 4.1 7.0 - - + -
94G ASN* 2.8 37.4 + - + +
96G SER* 1.3 82.8 - - - +
98G GLY* 1.3 66.5 + - - +
99G ALA 3.2 0.2 + - - -
100G GLU* 3.3 1.1 + - - +
101G VAL* 3.2 30.0 + - + +
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Residues in contact with GLY 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G HIS* 3.7 18.2 - - - -
91G MET* 3.2 25.7 + - - -
95G PRO 3.0 8.6 + - - -
97G TRP* 1.3 80.3 - - - +
99G ALA* 1.3 60.0 + - - +
101G VAL* 3.6 1.7 + - - +
102G ALA 3.2 15.4 + - - -
124G HIS* 3.5 12.3 + - - -
153G CYS* 3.5 8.1 - - - -
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Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G PRO 3.0 10.5 + - - +
96G SER* 3.7 8.7 - - - +
97G TRP 3.2 0.2 - - - -
98G GLY* 1.3 73.6 - - - +
100G GLU* 1.3 62.3 + - + +
102G ALA* 3.1 4.6 + - - +
103G HIS* 2.9 24.1 + - - +
152G GLN* 3.4 41.3 - - + +
153G CYS* 3.8 8.8 - - - +
156G ASN* 3.6 21.0 - - + +
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Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LYS* 3.1 36.7 + - + -
59G ILE* 4.1 21.5 - - + +
96G SER* 2.9 32.1 + - - +
97G TRP 4.3 1.3 - - - +
99G ALA* 1.3 75.4 - - + +
101G VAL* 1.3 58.3 + - - +
103G HIS* 3.9 8.5 - - + +
104G ALA* 3.1 26.9 + - - +
156G ASN* 5.9 3.1 - - - +
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Residues in contact with VAL 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LYS* 5.4 1.1 - - + +
58G LEU* 4.7 5.2 - - + -
59G ILE* 3.7 28.0 - - + +
62G TYR* 3.6 37.4 - - + +
85G THR* 4.4 0.4 - - + -
91G MET* 3.8 23.3 - - + -
97G TRP* 3.2 18.7 + - + +
98G GLY 3.7 3.6 - - - +
100G GLU* 1.3 75.3 - - - +
102G ALA* 1.3 60.3 + - - +
104G ALA* 3.3 3.9 + - - +
105G GLN* 2.8 44.7 + - - +
124G HIS* 4.1 2.5 - - - +
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Residues in contact with ALA 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLY 3.2 6.4 + - - +
99G ALA* 3.1 11.4 + - - +
101G VAL* 1.3 79.2 - - - +
103G HIS* 1.3 53.3 + - - +
105G GLN* 3.3 1.2 + - - +
106G LYS* 2.7 36.7 + - - +
122G LEU* 3.7 4.3 - - + +
124G HIS* 3.4 32.5 - - + +
153G CYS* 4.4 4.9 - - - +
156G ASN 3.4 12.1 - - - +
158G ALA 4.2 15.3 - - - +
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Residues in contact with HIS 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ALA 2.9 14.9 + - - +
100G GLU* 3.9 9.0 - - - +
102G ALA* 1.3 75.5 - - - +
104G ALA* 1.3 56.6 + - - +
106G LYS* 4.0 3.7 - - + +
107G THR* 2.7 53.6 + - + -
156G ASN* 3.1 39.1 + - + +
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Residues in contact with ALA 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ILE* 3.7 26.7 - - + +
62G TYR* 6.3 0.9 - - + -
63G GLU* 4.1 16.8 - - + +
100G GLU 3.1 17.8 + - - +
101G VAL* 3.7 4.7 - - - +
102G ALA 3.2 0.2 - - - -
103G HIS* 1.3 77.5 + - - +
105G GLN* 1.3 67.0 + - + +
107G THR* 3.6 6.0 + - - -
108G ILE* 3.4 26.4 + - - +
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Residues in contact with GLN 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G TYR* 2.9 26.8 + - - -
62G TYR* 4.2 18.3 - - + +
65G ILE* 5.0 0.2 - - - +
66G THR* 3.0 30.7 + - - +
83G LEU* 4.4 1.6 - - - +
85G THR* 2.5 23.6 + - - -
101G VAL* 2.8 25.7 + - - +
102G ALA 3.7 3.1 - - - +
104G ALA* 1.3 72.0 - - - +
106G LYS* 1.3 69.0 + - - +
108G ILE* 2.9 17.1 + - - +
109G MET* 3.2 24.0 + - + +
122G LEU* 3.6 8.4 - - + +
124G HIS* 3.0 25.1 - - - -
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Residues in contact with LYS 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLY* 5.0 0.2 - - - -
30G LEU* 4.1 30.7 - - + -
102G ALA 2.7 21.1 + - - +
103G HIS* 4.1 5.4 - - + +
105G GLN* 1.3 71.4 - - - +
107G THR* 1.3 62.5 + - - +
109G MET* 3.1 22.0 + - + -
110G GLU* 2.9 39.4 + - + +
121G ALA* 5.6 0.9 - - - +
122G LEU* 4.1 2.2 - - + +
157G GLY* 2.6 44.9 + - - +
159G ASP* 2.7 36.4 + - - -
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Residues in contact with THR 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G HIS* 2.7 43.3 + - + -
104G ALA* 3.9 8.0 - - - -
105G GLN 3.0 0.6 + - - -
106G LYS* 1.3 74.7 - - - +
108G ILE* 1.3 62.8 + - + +
110G GLU* 3.6 14.6 + - - +
111G LYS* 3.4 20.3 + - - +
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Residues in contact with ILE 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLU* 3.6 46.0 - - + +
66G THR* 3.9 21.8 - - + +
67G THR* 3.7 25.1 - - - +
70G MET* 4.5 1.1 - - + -
104G ALA 3.4 17.9 + - - +
105G GLN 2.9 5.8 + - - +
107G THR* 1.3 76.7 - - + +
109G MET* 1.3 66.0 + - - +
111G LYS* 3.3 10.1 + - + +
112G TYR* 3.2 37.8 + - + -
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Residues in contact with MET 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 3.7 7.5 - - + +
66G THR* 3.9 14.6 - - + -
70G MET* 4.3 20.9 - - + -
83G LEU* 3.8 26.2 - - + -
105G GLN* 3.2 24.2 + - + +
106G LYS* 3.1 17.8 + - + +
108G ILE* 1.3 75.7 - - - +
110G GLU* 1.3 57.5 + - - +
112G TYR* 3.4 2.9 + - - +
113G HIS* 3.0 28.2 + - - +
120G CYS* 4.1 18.7 - - - -
121G ALA* 4.6 8.5 - - - -
122G LEU* 3.6 45.3 - - + -
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Residues in contact with GLU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LEU* 3.9 29.4 - - + +
106G LYS* 2.9 30.1 + - + +
107G THR* 3.8 19.9 + - - +
108G ILE 3.3 0.2 - - - -
109G MET* 1.3 74.1 - - - +
111G LYS* 1.3 64.5 + - - +
113G HIS* 4.3 0.9 - - - -
114G ASP* 3.0 39.3 + - - +
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Residues in contact with LYS 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G THR 3.4 10.2 + - - +
108G ILE* 3.3 12.9 + - + +
110G GLU* 1.3 78.8 - - - +
112G TYR* 1.3 85.1 + - + +
114G ASP* 4.1 5.7 - - - +
115G GLU* 3.0 53.7 + - + +
116G TYR* 5.4 0.4 + - - -
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Residues in contact with TYR 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G THR* 4.0 14.8 + - + +
70G MET* 3.6 58.1 - - + -
71G GLU* 2.8 35.7 + - - +
74G VAL* 3.9 9.6 - - + -
108G ILE* 3.2 35.2 + - + -
109G MET 3.8 7.0 - - - +
110G GLU 3.2 0.4 - - - -
111G LYS* 1.3 97.6 + - + +
113G HIS* 1.3 59.7 + - - +
115G GLU* 3.3 0.6 + - - -
116G TYR* 2.8 62.2 + + - +
118G ILE* 4.2 3.8 - - + -
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Residues in contact with HIS 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 3.7 40.0 + - + +
31G ASP* 3.8 24.1 - - + +
109G MET 3.0 16.7 + - - +
110G GLU* 3.7 4.5 - - - +
112G TYR* 1.3 75.8 - - - +
114G ASP* 1.3 72.5 + - - +
117G GLY* 2.7 38.5 + - - +
118G ILE* 3.0 33.6 - - - +
120G CYS* 4.8 0.7 - - - -
4M LYS* 6.2 4.3 - - - -
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Residues in contact with ASP 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G GLU* 3.0 28.0 + - - +
111G LYS* 4.1 5.3 - - - +
113G HIS* 1.3 87.5 + - - +
115G GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 4.2 27.0 - - - +
111G LYS* 3.0 48.1 + - + +
113G HIS 3.2 0.8 - - - -
114G ASP* 1.3 79.7 - - + +
116G TYR* 1.3 100.2 + - + +
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Residues in contact with TYR 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E LEU* 3.4 33.6 - - + +
14F THR* 5.4 1.2 - - - +
16F TYR* 3.4 41.5 - - + -
20F LEU* 3.6 22.0 - - + +
71G GLU* 5.0 3.5 + - - -
74G VAL* 3.6 20.7 - - + +
111G LYS* 5.4 0.6 + - - -
112G TYR* 2.8 62.2 + + - +
115G GLU* 1.3 109.7 + - + +
117G GLY* 1.3 60.6 + - - +
118G ILE* 4.0 3.1 - - + +
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Residues in contact with GLY 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 4.7 2.0 - - - -
31G ASP* 5.7 0.3 - - - +
79G PRO 4.7 0.3 - - - +
113G HIS* 2.7 31.2 + - - -
115G GLU 3.9 0.4 - - - -
116G TYR* 1.3 72.8 - - - +
118G ILE* 1.3 65.6 + - - +
119G LYS* 3.5 13.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il