Contacts of the helix formed by residues 84 - 103 (chain G) in PDB entry 2HOI
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 ALA 84 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F T 2.8 43.3 + - - +
14F A 4.8 6.1 - - - +
82G GLY 3.7 1.6 + - - -
83G LEU* 1.3 75.7 - - - +
85G VAL* 1.3 64.6 + - - +
86G LYS 3.3 5.8 - - - +
87G THR* 3.2 6.8 + - - +
88G ILE* 3.0 21.2 + - - +
129G GLU* 3.3 19.7 - - + +
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Residues in contact with VAL 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 4.0 18.4 - - + +
84G ALA* 1.3 70.1 - - - +
86G LYS* 1.3 57.6 + - + +
88G ILE* 3.2 10.5 + - - +
89G GLN* 2.9 45.1 + - - +
117G MET* 4.8 6.0 - - + +
120G ILE* 4.6 3.1 - - + +
121G ARG* 3.8 37.9 - - + +
124G ASN* 3.6 28.9 - - + +
129G GLU* 2.7 22.3 + - - +
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Residues in contact with LYS 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 5.4 7.7 + - - +
21E A 4.6 4.6 - - - +
22E T 5.1 0.2 + - - -
13F T 4.3 8.3 - - + -
14F A 3.6 48.0 + - + +
15F A 3.0 43.3 - - - +
16F T 4.5 6.2 + - - -
84G ALA* 3.3 1.8 - - + +
85G VAL* 1.3 75.0 - - + +
87G THR* 1.3 61.5 + - - +
89G GLN* 3.3 28.3 + - - +
90G GLN* 2.8 30.5 + - - +
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Residues in contact with THR 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F A 3.3 17.5 - - + +
13F T 2.8 67.5 + - + +
83G LEU* 3.9 22.9 - - + -
84G ALA* 3.2 9.4 + - - +
86G LYS* 1.3 77.3 - - - +
88G ILE* 1.3 61.9 + - - +
90G GLN* 3.2 2.6 + - - +
91G HIS* 3.0 38.9 + - + +
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Residues in contact with ILE 88 (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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75G LEU* 3.9 30.4 - - + +
78G LEU* 4.0 23.1 - - + -
79G GLN* 3.9 22.0 - - + +
83G LEU* 3.7 19.1 - - + +
84G ALA 3.0 16.8 + - - +
85G VAL* 3.2 8.7 + - - +
87G THR* 1.3 76.8 - - - +
89G GLN* 1.3 61.2 + - - +
91G HIS* 3.4 4.0 + - - +
92G LEU* 3.1 21.1 + - - +
117G MET* 4.0 19.5 - - + -
120G ILE* 3.9 26.9 - - + -
124G ASN* 4.6 1.1 - - - +
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Residues in contact with GLN 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E T 5.4 0.3 - - - +
85G VAL* 2.9 19.7 + - - +
86G LYS* 3.3 39.2 + - - +
88G ILE* 1.3 71.8 - - - +
90G GLN* 1.3 55.7 + - - +
92G LEU* 3.2 10.5 + - + +
93G GLY* 2.7 34.0 + - - -
117G MET* 3.9 8.3 - - + +
121G ARG* 2.5 41.9 + - - +
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Residues in contact with GLN 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E T 3.7 17.0 + - - +
23E T 2.5 30.7 + - - +
13F T 3.6 32.3 + - + +
14F A 3.1 15.2 - - - +
44G MET* 4.0 14.6 - - + +
48G VAL* 4.8 0.7 - - + -
86G LYS 2.8 16.8 + - - +
87G THR 3.3 8.7 - - - +
89G GLN* 1.3 73.8 - - - +
91G HIS* 1.3 64.1 + - + +
93G GLY* 3.4 1.4 + - - -
94G GLN* 3.1 63.4 + - + +
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Residues in contact with HIS 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F A 3.9 21.7 + - - -
13F T 4.9 3.7 - - + +
44G MET* 5.7 1.4 - - - +
47G SER 5.8 0.2 - - - -
48G VAL* 3.6 40.3 - - + +
51G SER* 4.0 13.9 - - - -
74G TYR* 2.9 31.1 + - + -
75G LEU* 5.3 0.9 - - + -
78G LEU* 3.5 26.9 - - + +
83G LEU* 4.5 1.0 - - + +
87G THR* 3.0 40.5 + - + +
88G ILE 3.6 7.9 - - - +
89G GLN 3.3 0.2 - - - -
90G GLN* 1.3 79.2 - - + +
92G LEU* 1.3 63.2 + - - +
94G GLN 3.3 1.9 + - - -
95G LEU* 3.2 22.0 + - - +
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Residues in contact with LEU 92 (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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71G VAL* 4.9 3.8 - - + -
75G LEU* 4.4 15.3 - - + +
88G ILE 3.1 13.0 + - - +
89G GLN* 3.4 11.9 - - + +
91G HIS* 1.3 75.6 - - - +
93G GLY* 1.3 56.9 + - - +
95G LEU* 3.0 9.9 + - + +
96G ASN* 2.9 35.8 + - - +
107G PRO* 4.3 8.5 - - + -
108G SER* 3.2 35.0 - - - +
113G VAL* 4.1 15.0 - - + -
117G MET* 3.7 34.5 - - + -
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Residues in contact with GLY 93 (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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21E A 5.9 3.4 - - - +
22E T 4.2 21.7 + - - +
89G GLN 2.7 19.8 + - - -
90G GLN 3.4 2.0 + - - -
92G LEU* 1.3 71.5 - - - +
94G GLN* 1.3 57.1 + - - +
96G ASN* 3.2 13.3 + - - +
97G MET* 2.9 29.5 + - - +
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Residues in contact with GLN 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E T 4.8 4.9 - - + +
23E T 3.7 20.8 - - - +
41G THR* 3.8 15.8 + - - +
44G MET* 3.9 4.2 - - - +
45G LEU* 3.2 42.7 - - + +
48G VAL* 3.8 28.3 - - + -
90G GLN* 3.1 39.7 + - - +
91G HIS 3.6 8.3 - - - +
92G LEU 3.2 0.2 - - - -
93G GLY* 1.3 75.9 - - - +
95G LEU* 1.3 57.6 + - - +
97G MET* 3.3 14.5 + - - +
98G LEU* 3.0 29.8 + - - +
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LEU* 6.3 0.2 - - + -
48G VAL* 4.1 20.9 - - + +
49G CYS* 5.5 3.4 - - - -
52G TRP* 4.2 42.8 - - + -
66G ALA* 5.0 1.1 - - + -
71G VAL* 4.4 24.5 - - + -
74G TYR* 4.6 11.9 - - + -
75G LEU* 5.8 0.9 - - + -
91G HIS 3.2 11.9 + - - +
92G LEU* 3.0 12.2 + - - +
94G GLN* 1.3 76.2 - - - +
96G ASN* 1.3 66.3 + - - +
98G LEU* 3.6 10.4 + - + -
99G HIS* 2.6 42.3 + - + -
107G PRO* 4.0 14.8 - - + -
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Residues in contact with ASN 96 (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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92G LEU* 2.9 20.9 + - - +
93G GLY* 3.4 14.8 - - - +
95G LEU* 1.3 74.0 - - - +
97G MET* 1.3 60.0 + - - +
99G HIS 3.4 0.7 + - - -
100G ARG* 2.9 32.7 + - - +
106G ARG* 3.5 34.2 - - + +
107G PRO* 3.3 9.9 - - - +
108G SER* 2.9 49.6 + - - -
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Residues in contact with MET 97 (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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22E T 3.2 50.7 + - - +
30G MET* 3.8 30.3 - - + -
37G PHE* 4.7 12.1 - - + -
41G THR* 4.5 11.9 - - + -
42G TRP* 5.6 2.5 - - + -
45G LEU* 4.1 23.1 - - + -
93G GLY 2.9 17.2 + - - +
94G GLN* 3.3 17.2 + - - +
96G ASN* 1.3 76.8 - - - +
98G LEU* 1.3 72.1 + - - +
100G ARG* 3.8 3.4 - - - +
101G ARG* 3.0 36.1 + - + +
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Residues in contact with LEU 98 (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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27G LEU* 4.5 18.7 - - + +
30G MET* 4.9 10.3 - - + -
45G LEU* 4.3 20.4 - - + -
49G CYS* 3.8 27.1 - - - -
52G TRP* 6.2 0.4 - - + -
63G TRP* 4.3 15.9 - - + -
64G PHE* 4.3 20.4 - - + -
94G GLN 3.0 13.8 + - - +
95G LEU* 3.9 11.0 - - + +
97G MET* 1.3 84.7 - - - +
99G HIS* 1.3 60.5 + - + +
101G ARG* 4.0 3.9 - - - +
102G SER* 2.7 35.6 + - - +
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Residues in contact with HIS 99 (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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52G TRP* 5.7 0.4 - - - -
63G TRP 5.0 1.6 - - - -
64G PHE* 4.0 19.6 - + - -
65G PRO* 3.8 6.1 - - + +
66G ALA* 2.9 48.7 + - + +
95G LEU* 2.6 36.5 + - + +
96G ASN 3.8 2.5 - - - +
98G LEU* 1.3 81.1 - - + +
100G ARG* 1.3 61.0 + - - +
102G SER* 3.1 6.5 + - - -
103G GLY 3.0 4.7 + - - -
104G LEU* 2.7 46.6 + - + +
105G PRO 3.8 24.2 - - - +
106G ARG* 4.4 1.6 - - - -
107G PRO* 4.0 14.5 - - + +
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Residues in contact with ARG 100 (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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20E C 5.3 1.0 + - - -
21E A 4.2 10.7 + - - -
22E T 6.1 0.4 - - - +
96G ASN 2.9 18.3 + - - +
97G MET* 3.9 4.7 - - - +
99G HIS* 1.3 73.9 - - - +
101G ARG* 1.3 67.0 + - + +
103G GLY* 2.9 19.6 + - - -
104G LEU 3.8 8.0 + - - -
106G ARG* 3.5 47.4 - - - +
109G ASP* 4.5 5.7 + - - -
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Residues in contact with ARG 101 (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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22E T 4.5 7.7 + - - -
26G ASN* 3.2 9.8 - - - +
27G LEU* 5.9 1.1 - - + -
30G MET* 3.7 39.0 - - + -
37G PHE* 3.9 10.6 - - + -
97G MET* 3.0 28.2 + - + +
98G LEU 4.1 2.9 - - - +
100G ARG* 1.3 83.4 - - + +
102G SER* 1.3 57.8 + - - +
103G GLY 3.1 1.0 + - - -
111H ASN* 2.7 51.2 + - - +
114H SER* 2.9 26.5 + - - -
115H LEU* 3.7 14.3 - - - +
118H ARG* 4.2 28.1 - - - +
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Residues in contact with SER 102 (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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23G VAL* 3.4 23.1 - - - +
26G ASN* 2.9 23.1 + - - -
27G LEU* 3.7 16.9 - - - +
64G PHE* 3.2 17.7 - - - -
98G LEU* 2.7 22.0 + - - +
99G HIS 3.1 8.4 + - - -
101G ARG* 1.3 75.2 - - - +
103G GLY* 1.3 60.2 + - - +
104G LEU* 3.8 21.3 - - - -
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Residues in contact with GLY 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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23G VAL* 5.2 1.6 - - - +
26G ASN* 4.2 7.2 - - - -
100G ARG 2.9 16.3 + - - -
101G ARG 3.1 1.4 + - - -
102G SER* 1.3 79.7 - - - +
104G LEU* 1.3 63.8 + - - +
105G PRO* 4.6 1.0 - - - +
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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
------------------------------------------------------------
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