Contacts of the helix formed by residues 94 - 110 (chain H) 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 PHE 94 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G ASN 3.9 14.8 - - - -
236G LYS* 3.4 30.5 - - + +
238G LEU 3.6 11.4 - - - -
239G ALA* 3.4 37.5 - - - -
240G HIS* 5.0 2.2 - + - -
417G PHE* 3.5 35.9 - + + -
418G GLU* 5.8 5.6 - - + -
88H TYR* 3.9 3.6 - - - -
91H GLY 4.6 10.3 - - - -
93H ILE* 1.3 81.3 - - - +
95H LEU* 1.3 69.9 + - - +
96H PRO* 3.7 9.6 - - + -
97H ASN* 2.9 33.3 + - - +
98H VAL* 3.4 4.9 + - - +
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Residues in contact with LEU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G LEU* 4.5 15.9 - - + -
229G ILE* 4.9 1.6 - - + -
236G LYS 3.0 8.7 + - - -
237G ASN* 3.6 35.7 - - + +
88H TYR* 3.3 14.9 - - + +
94H PHE* 1.3 69.3 - - - +
96H PRO* 1.4 71.3 - - + +
98H VAL* 2.8 24.5 + - + +
99H MET* 2.8 34.9 + - + -
142H ILE* 3.7 49.4 - - + -
146H LEU* 4.7 7.9 - - + -
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Residues in contact with PRO 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G VAL 4.2 4.0 - - - +
177G LEU* 3.1 28.5 - - - +
178G ARG* 4.4 0.2 - - - -
179G ASN* 3.3 37.5 - - - +
237G ASN 3.2 23.3 - - - +
238G LEU* 4.1 13.0 - - + -
239G ALA 5.5 0.4 - - - +
94H PHE* 3.5 14.4 - - + -
95H LEU* 1.4 87.1 - - + +
97H ASN* 1.3 55.8 + - - +
99H MET* 3.6 2.1 - - + +
100H MET* 3.0 33.7 + - - +
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Residues in contact with ASN 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ASN* 4.4 13.0 + - - +
417G PHE* 3.1 25.1 - - - -
48H PHE* 4.9 5.2 - - + +
93H ILE* 3.8 23.3 - - + +
94H PHE* 2.9 37.2 + - - +
96H PRO* 1.3 74.7 - - - +
98H VAL* 1.3 60.3 + - - +
100H MET* 3.4 18.1 + - + +
101H SER* 2.9 34.0 + - - -
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Residues in contact with VAL 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H MET* 3.9 8.5 - - + +
84H VAL* 3.7 16.4 - - + +
85H ILE* 5.2 9.4 - - + -
88H TYR* 3.3 46.9 - - + -
93H ILE* 4.0 8.2 - - + +
94H PHE 3.8 2.9 - - - +
95H LEU* 2.8 17.2 + - + +
97H ASN* 1.3 71.7 - - - +
99H MET* 1.3 54.0 + - + +
101H SER* 3.1 4.0 + - - -
102H ALA* 2.7 38.1 + - + +
145H ALA 5.8 1.3 - - - +
146H LEU* 4.4 22.7 - - + +
149H ALA* 5.4 4.0 - - + -
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Residues in contact with MET 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G LEU* 3.2 43.1 - - + +
178G ARG* 3.8 35.0 - - + +
95H LEU* 2.8 38.8 + - + +
96H PRO 3.6 2.2 - - - +
98H VAL* 1.3 73.1 - - - +
100H MET* 1.3 54.7 + - - +
102H ALA* 3.1 4.2 + - + +
103H ASP* 2.8 42.7 + - - +
141H ASN* 4.7 11.4 - - + +
142H ILE* 5.1 4.5 - - - -
145H ALA* 3.7 29.8 - - + -
146H LEU* 6.3 0.4 - - - -
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Residues in contact with MET 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G ARG* 3.6 32.9 - - + +
179G ASN* 4.8 8.1 - - - -
48H PHE 5.7 1.3 - - - +
49H GLU 4.1 21.8 - - - +
50H GLY* 3.6 20.4 - - - +
96H PRO 3.0 17.9 + - - +
97H ASN* 3.7 19.3 - - + +
99H MET* 1.3 74.8 - - - +
101H SER* 1.3 62.1 + - - +
103H ASP* 3.4 10.1 + - - +
104H ALA* 3.3 17.2 + - - +
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Residues in contact with SER 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 2.8 29.5 + - - +
48H PHE 3.2 16.1 + - - -
50H GLY* 4.1 1.0 + - - -
81H MET* 3.6 11.3 - - - +
84H VAL* 3.4 26.8 - - - +
97H ASN 2.9 17.4 + - - -
98H VAL 3.4 4.5 - - - -
100H MET* 1.3 77.2 - - - +
102H ALA* 1.3 55.4 + - - +
104H ALA* 3.4 3.3 + - - +
105H MET* 2.9 28.4 + - - +
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H MET* 3.5 13.8 - - + +
98H VAL* 2.7 18.2 + - + +
99H MET* 3.1 12.5 + - + +
101H SER* 1.3 70.4 - - - +
103H ASP* 1.3 62.3 + - - +
105H MET* 3.6 8.0 - - + +
106H LEU* 2.9 36.2 + - + +
145H ALA* 4.4 26.9 - - + +
148H ARG* 6.1 1.8 - - + -
149H ALA* 4.8 3.4 - - + +
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Residues in contact with ASP 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G TYR* 4.4 7.6 + - - -
178G ARG* 2.9 43.4 + - - -
52H GLU* 5.1 2.8 - - - +
99H MET* 2.8 29.9 + - - +
100H MET* 3.6 11.2 - - - +
101H SER 3.3 0.2 - - - -
102H ALA* 1.3 77.2 - - - +
104H ALA* 1.3 57.1 + - - +
106H LEU* 3.6 12.7 + - - +
107H GLU* 3.2 28.9 + - - +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 4.7 5.4 - - - +
50H GLY* 3.9 25.1 - - - +
52H GLU* 4.0 25.1 + - + +
55H VAL* 3.9 22.0 - - + +
100H MET 3.3 11.1 + - - +
101H SER 3.7 6.7 - - - +
102H ALA 3.3 0.2 - - - -
103H ASP* 1.3 76.3 - - - +
105H MET* 1.3 63.5 + - - +
106H LEU 3.3 0.2 - - - -
107H GLU* 3.9 1.9 - - - +
108H GLY* 3.2 18.9 + - - -
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Residues in contact with MET 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 4.7 7.8 - - + +
77H LEU* 4.0 29.6 - - + +
78H MET* 5.2 7.0 - - - +
81H MET* 3.7 29.2 - - - +
101H SER 2.9 17.8 + - - +
102H ALA* 3.3 10.0 + - + +
104H ALA* 1.3 77.9 - - - +
106H LEU* 1.3 73.7 + - + +
108H GLY* 3.4 2.2 + - - -
109H ILE* 3.1 51.0 + - + +
148H ARG* 3.4 32.8 - - + +
149H ALA* 4.1 5.4 - - + +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ALA* 2.9 23.0 + - + +
103H ASP* 3.8 11.7 - - - +
104H ALA 3.3 0.2 - - - -
105H MET* 1.3 90.2 - - + +
107H GLU* 1.3 59.7 + - - +
108H GLY 3.1 1.1 + - - -
109H ILE* 3.4 17.8 + - + +
110H GLU* 3.5 18.1 + - - +
113H LYS* 6.3 0.9 - - - +
148H ARG* 4.5 37.7 - - + +
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Residues in contact with GLU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLU* 3.5 38.2 - - + +
53H ASP* 4.3 5.7 - - - +
55H VAL* 5.4 0.4 - - - -
56H VAL* 4.0 15.6 - - + +
103H ASP 3.2 17.8 + - - +
104H ALA 4.0 1.3 - - - +
105H MET 3.4 0.6 - - - -
106H LEU* 1.3 74.8 - - - +
108H GLY* 1.3 57.4 + - - +
110H GLU* 4.5 17.4 - - + +
111H TYR* 4.0 16.6 + - - +
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Residues in contact with GLY 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H VAL* 4.0 18.4 - - - -
56H VAL* 5.2 0.7 - - - -
59H LEU* 3.7 12.0 - - - +
77H LEU* 3.2 19.5 - - - +
104H ALA 3.2 14.5 + - - -
105H MET 3.4 2.9 + - - -
106H LEU 3.1 0.4 - - - -
107H GLU* 1.3 79.5 - - - +
109H ILE* 1.3 58.4 + - - +
110H GLU 3.6 0.2 - - - -
111H TYR* 4.2 1.7 + - - -
112H CYS* 3.2 19.4 + - - -
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Residues in contact with ILE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H ILE* 3.8 28.1 - - + +
77H LEU* 3.8 15.7 - - + -
78H MET* 6.5 0.9 - - - -
105H MET* 3.1 43.4 + - + +
106H LEU* 3.4 12.5 + - + +
108H GLY* 1.3 77.6 - - - +
110H GLU* 1.3 57.7 + - - +
111H TYR 3.2 1.6 - - - -
112H CYS* 3.0 23.9 + - - +
113H LYS* 3.2 29.4 + - + +
120H PRO* 5.5 7.5 - - + +
148H ARG 5.5 0.7 - - - +
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU 3.5 14.1 + - - +
107H GLU* 4.6 16.2 - - + +
109H ILE* 1.3 75.6 - - - +
111H TYR* 1.3 61.6 + - - +
112H CYS 3.3 0.2 - - - -
113H LYS* 3.3 45.8 + - + +
114H GLU* 3.5 14.4 - - - +
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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