Contacts of the helix formed by residues 76 - 90 (chain P) 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 ALA 76 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ILE* 3.8 14.6 - - + +
43P ILE* 3.8 31.2 - - + -
44P ALA* 4.7 4.0 - - - -
47P ILE* 4.3 2.3 - - - +
59P LEU* 4.7 0.2 - - + -
72P LEU* 2.9 34.1 + - + +
75P ASP* 1.3 79.3 - - - +
77P LEU* 1.3 60.9 + - + +
78P MET 3.5 0.9 - - - -
79P VAL* 3.4 1.8 + - - +
80P GLY* 3.0 27.0 + - - -
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Residues in contact with LEU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P ILE* 3.5 28.0 - - + -
47P ILE* 3.5 18.0 - - + +
55P VAL* 3.9 17.0 - - + -
59P LEU* 4.2 7.9 - - + -
72P LEU 3.0 12.4 + - - +
73P ILE* 3.6 14.1 - - + +
76P ALA* 1.3 75.5 - - + +
78P MET* 1.3 59.5 + - - +
80P GLY* 3.9 1.0 - - - -
81P MET* 3.0 29.2 + - - +
105P MET* 4.1 19.5 - - + +
108P GLY* 3.7 31.2 - - - +
109P ILE* 3.9 15.3 - - + +
112P CYS* 4.3 10.3 - - - -
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Residues in contact with MET 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P ILE* 2.9 35.4 + - + +
74P ASP* 3.6 28.9 + - - +
77P LEU* 1.3 71.8 - - - +
79P VAL* 1.3 61.0 + - + +
81P MET* 3.6 3.9 - - + +
82P GLY* 2.8 26.0 + - - -
105P MET* 4.5 14.8 - - - +
109P ILE* 5.4 4.7 - - - -
148P ARG 3.9 8.5 - - - +
149P ALA* 3.4 20.0 - - - +
150P ASN* 4.2 0.9 - - - -
151P GLY* 3.3 37.7 - - - +
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Residues in contact with VAL 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P LEU 5.9 0.2 - - - +
35P PRO* 3.7 33.9 - - + -
74P ASP 3.4 19.2 + - - +
75P ASP* 3.5 20.2 - - - +
76P ALA 3.4 2.6 + - - +
77P LEU 3.3 0.6 - - - -
78P MET* 1.3 75.1 - - + +
80P GLY* 1.3 64.5 + - - +
82P GLY* 3.4 2.6 + - - -
83P VAL* 3.3 23.4 + - + +
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Residues in contact with GLY 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P TYR* 6.0 0.2 - - - -
44P ALA* 3.7 31.5 - - - +
47P ILE* 3.6 9.7 - - - +
48P PHE* 5.4 0.3 - - - +
76P ALA 3.0 16.2 + - - -
77P LEU 3.9 1.1 - - - -
79P VAL* 1.3 77.7 - - - +
81P MET* 1.3 59.8 + - - +
83P VAL* 3.4 20.3 - - - +
84P VAL* 3.5 13.2 + - - +
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Residues in contact with MET 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P ILE* 3.8 11.9 - - + +
77P LEU 3.0 18.4 + - - +
78P MET* 3.6 9.6 - - + +
79P VAL 3.2 0.2 - - - -
80P GLY* 1.3 75.9 - - - +
82P GLY* 1.3 58.0 + - - +
83P VAL 3.2 1.6 - - - -
84P VAL* 3.1 15.1 + - + +
85P ILE* 3.0 36.9 + - + +
98P VAL* 3.8 15.5 - - + +
101P SER* 4.0 24.0 - - - +
102P ALA* 3.7 30.3 - - + +
105P MET* 3.9 20.4 - - - +
149P ALA* 4.0 32.8 - - + +
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Residues in contact with GLY 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P MET 2.8 16.7 + - - -
79P VAL* 3.4 3.6 + - - -
80P GLY 3.4 0.4 - - - -
81P MET* 1.3 74.0 - - - +
83P VAL* 1.3 62.9 + - - +
85P ILE* 3.6 12.7 + - - +
86P ARG* 3.1 23.9 + - - +
149P ALA 5.3 0.4 - - - -
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Residues in contact with VAL 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ALA* 4.4 12.6 - - + +
33P LEU* 3.7 48.5 - - + +
34P TYR* 4.6 11.0 - - + +
35P PRO* 4.7 5.8 - - + -
48P PHE* 4.9 2.0 - - + -
79P VAL* 3.3 16.4 + - + +
80P GLY* 3.4 12.8 - - - +
81P MET 3.2 0.4 - - - -
82P GLY* 1.3 75.2 - - - +
84P VAL* 1.3 63.6 + - + +
86P ARG* 3.2 7.8 + - - +
87P LEU* 3.0 41.3 + - + +
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Residues in contact with VAL 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P ILE* 4.1 3.1 - - + -
48P PHE* 3.7 30.7 - - + -
80P GLY 3.5 13.7 + - - +
81P MET* 3.1 16.2 + - + +
83P VAL* 1.3 75.8 - - + +
85P ILE* 1.3 62.1 + - - +
87P LEU* 3.5 1.3 + - - -
88P TYR* 3.1 20.6 + - - +
93P ILE* 3.5 23.8 - - + +
98P VAL* 3.9 16.6 - - + -
101P SER* 3.5 38.6 - - - +
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Residues in contact with ILE 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P MET* 3.0 29.9 + - + +
82P GLY* 3.8 9.9 - - - +
83P VAL 3.2 0.2 - - - -
84P VAL* 1.3 74.4 - - - +
86P ARG* 1.3 62.3 + - - +
88P TYR* 3.3 9.4 + - + +
89P ASP* 2.8 44.0 + - - +
98P VAL* 5.4 4.0 - - + -
146P LEU* 3.6 27.8 - - + -
149P ALA* 3.1 48.7 - - + +
150P ASN* 4.2 13.7 - - - +
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Residues in contact with ARG 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P LEU* 3.2 42.6 - - + +
82P GLY 3.1 15.7 + - - +
83P VAL* 3.3 11.9 - - - +
85P ILE* 1.3 75.6 - - - +
87P LEU* 1.3 57.6 + - - +
89P ASP* 3.0 13.1 + - - +
90P GLU* 2.8 56.4 + - - +
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Residues in contact with LEU 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PRO 4.1 1.3 - - - +
29P ALA* 3.9 15.0 - - + +
30P ALA* 3.8 22.9 - - + +
33P LEU* 3.8 20.0 - - + -
48P PHE* 3.6 31.9 - - + -
83P VAL* 3.0 22.6 + - + +
84P VAL 4.0 3.8 - - - +
86P ARG* 1.3 75.6 - - - +
88P TYR* 1.3 56.0 + - - +
90P GLU* 3.5 16.8 + - - +
91P GLY 3.0 6.1 + - - -
92P VAL* 2.8 57.8 + - + -
93P ILE* 3.4 10.0 + - + -
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Residues in contact with TYR 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236O LYS* 2.6 69.1 + - + +
237O ASN* 2.6 22.1 + - - -
84P VAL 3.1 14.8 + - - +
85P ILE* 3.4 11.2 - - - +
86P ARG 3.2 0.2 - - - -
87P LEU* 1.3 76.3 - - - +
89P ASP* 1.3 57.8 + - - +
91P GLY* 3.0 10.6 + - - -
93P ILE* 3.7 19.4 - - + +
94P PHE 3.9 2.0 - - - -
95P LEU* 3.5 22.4 - - + +
98P VAL* 3.6 24.9 - - + -
142P ILE* 4.8 7.3 - - + +
146P LEU* 4.4 26.5 - - + -
230P GLU* 5.0 7.0 + - - -
231P ALA* 6.0 1.5 - - + +
232P ALA* 5.9 5.6 - - + -
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Residues in contact with ASP 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236O LYS* 3.5 15.2 + - - +
85P ILE* 2.8 37.8 + - - +
86P ARG* 3.0 10.7 + - - +
88P TYR* 1.3 80.2 - - - +
90P GLU* 1.3 62.2 + - + +
91P GLY 3.2 0.7 + - - -
146P LEU* 6.4 0.2 - - - -
232P ALA* 4.4 17.5 - - - +
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Residues in contact with GLU 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P LYS* 4.0 28.8 + - - +
29P ALA* 5.8 0.5 - - - +
33P LEU* 5.1 1.3 - - - +
86P ARG* 2.8 58.6 + - + +
87P LEU* 3.8 20.6 - - - +
88P TYR 3.3 0.2 - - - -
89P ASP* 1.3 77.4 - - + +
91P GLY* 1.3 61.1 + - - +
92P VAL* 3.5 14.9 + - + +
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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
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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