Contacts of the helix formed by residues 72 - 89 (chain P) in PDB entry 1SXG
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 72 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P ASP* 2.8 21.2 + - + +
71P SER* 1.3 75.5 - - - +
73P ILE* 1.3 75.4 + - - +
74P PHE* 2.8 28.4 + - - +
75P TYR* 3.0 41.2 + - + +
76P ALA* 3.0 12.2 + - - +
221P TYR* 5.6 8.0 - - - -
247P THR* 5.6 4.7 + - - +
275P ASP* 4.9 1.6 + - - +
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Residues in contact with ILE 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F SER 5.1 2.9 - - - +
73F ILE* 4.6 13.9 - - + -
278F ARG* 4.6 4.5 - - - +
71P SER 3.3 4.2 + - - +
72P ASN* 1.3 78.5 - - - +
74P PHE* 1.3 65.3 + - + +
76P ALA* 3.4 6.4 + - + +
77P GLU* 2.9 36.5 + - - +
247P THR* 5.3 5.4 - - + -
248P ASP* 4.7 2.5 - - + -
249P GLU* 4.0 31.2 - - + +
275P ASP* 5.3 2.7 - - - +
277P THR* 3.6 26.2 - - + +
278P ARG* 4.4 26.7 - - - +
279P LEU* 3.9 29.6 - - + -
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Residues in contact with PHE 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ASN* 2.8 20.1 - - - +
73P ILE* 1.3 75.4 - - + +
75P TYR* 1.3 82.4 + + - +
77P GLU* 3.1 4.1 + - - +
78P LEU* 2.8 39.9 + - + +
146P ALA* 3.8 23.1 - - + -
161P TYR* 5.2 0.2 - - - -
275P ASP* 3.4 38.4 - - + +
277P THR* 3.9 6.3 - - - +
292P GLN* 3.1 49.8 - - + -
294P MET* 3.8 27.6 - - + -
297P ILE* 6.0 1.6 - - + -
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Residues in contact with TYR 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ILE* 4.5 13.4 - - + +
68P PRO* 3.8 37.7 - - + -
69P ASP 4.3 7.4 - - - +
70P ILE* 5.9 0.4 - - - -
72P ASN* 3.0 39.9 + - + +
74P PHE* 1.3 102.9 - + - +
76P ALA* 1.3 61.6 + - - +
78P LEU* 3.9 2.5 - - + +
79P ALA* 3.1 24.8 + - - +
123P MET* 3.6 35.8 - - + +
124P SER 4.4 9.4 + - - -
125P GLY* 4.8 6.5 - - - -
146P ALA* 3.4 21.9 + - + +
161P TYR* 5.2 0.5 + - - -
191P ILE* 5.8 3.6 - - - +
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Residues in contact with ALA 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 3.9 13.8 - - + +
71F SER* 3.4 35.8 - - - +
70P ILE* 4.1 20.1 + - + +
72P ASN 3.0 11.1 + - - +
73P ILE* 3.7 12.6 - - + +
75P TYR* 1.3 79.6 - - - +
77P GLU* 1.3 62.4 + - - +
79P ALA* 3.6 4.7 + - - +
80P ARG* 3.2 15.6 + - - +
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Residues in contact with GLU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F SER* 4.1 5.8 - - - -
73P ILE* 2.9 22.3 + - - +
74P PHE 3.8 0.4 - - - +
76P ALA* 1.3 76.2 - - + +
78P LEU* 1.3 65.6 + - - +
80P ARG* 3.0 8.8 + - - +
81P GLY* 2.8 21.3 + - - -
277P THR* 3.1 15.2 + - - +
278P ARG* 2.8 61.3 + - - +
294P MET* 3.7 32.2 - - - +
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Residues in contact with LEU 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P PHE* 2.8 26.6 + - + +
75P TYR* 4.1 4.9 - - - +
77P GLU* 1.3 75.3 - - - +
79P ALA* 1.3 65.4 + - - +
81P GLY* 3.0 3.7 + - - +
82P ILE* 2.9 31.4 + - + +
123P MET* 3.8 24.7 - - + -
145P ALA* 4.3 5.6 - - + -
146P ALA* 3.9 26.9 - - + -
294P MET* 3.4 47.7 - - + +
297P ILE* 3.5 22.9 - - + -
298P GLY 4.4 1.8 - - - +
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Residues in contact with ALA 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 4.6 6.7 - - + -
65P VAL* 5.0 1.8 - - + -
67P ILE* 4.4 13.2 - - + -
70P ILE* 6.2 0.9 - - + -
75P TYR 3.1 17.6 + - - +
76P ALA* 3.8 6.1 - - - +
78P LEU* 1.3 79.5 - - - +
80P ARG* 1.3 53.3 + - - +
82P ILE* 2.8 32.0 + - - +
83P GLU* 2.9 17.9 + - - +
95P LEU* 4.0 25.3 - - + +
123P MET* 4.8 4.2 - - + +
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Residues in contact with ARG 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ASP* 3.7 17.9 + - - +
70F ILE* 4.9 3.3 - - + +
71F SER* 3.7 22.4 - - - +
97F ASN* 5.2 3.5 - - - +
99F ASP* 3.1 40.6 + - - +
76P ALA 3.2 11.8 + - - +
77P GLU* 3.0 11.1 + - - +
79P ALA* 1.3 76.9 - - - +
81P GLY* 1.3 58.6 + - - +
83P GLU* 2.9 37.0 + - + +
84P ASP* 2.6 51.5 + - - +
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Residues in contact with GLY 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P GLU 2.8 16.1 + - - -
78P LEU* 3.0 5.1 + - - -
80P ARG* 1.3 73.1 - - - +
82P ILE* 1.3 61.7 + - - +
84P ASP* 3.4 10.5 + - - +
85P ILE* 3.0 29.4 + - - +
294P MET* 5.3 11.2 - - - -
295P TYR* 5.7 4.2 - - - -
298P GLY* 5.5 2.7 - - - -
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Residues in contact with ILE 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P VAL* 4.2 9.4 - - + -
78P LEU* 2.9 29.0 + - + +
79P ALA* 2.8 17.6 + - - +
81P GLY* 1.3 75.8 - - - +
83P GLU* 1.3 58.2 + - - +
85P ILE* 3.5 4.6 + - - +
86P ALA* 2.9 27.9 + - - +
93P ILE* 3.7 19.3 - - + -
121P ILE* 4.0 28.3 - - + -
123P MET* 4.9 7.4 - - + -
145P ALA* 5.5 0.4 - - + -
297P ILE* 5.1 1.6 - - + -
298P GLY* 3.4 31.6 - - - +
301P ALA* 5.1 2.0 - - + -
302P MET* 3.8 15.2 - - + +
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Residues in contact with GLU 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F SER* 4.9 0.2 - - - -
97F ASN* 2.7 46.5 + - + +
99F ASP* 5.4 2.0 - - - +
104F LYS* 4.9 10.8 + - - +
79P ALA 2.9 15.7 + - - +
80P ARG* 2.9 27.9 + - + +
82P ILE* 1.3 75.8 - - - +
84P ASP* 1.3 65.7 + - - +
86P ALA* 2.9 16.8 + - - +
87P THR* 3.1 18.8 + - - +
93P ILE* 2.7 46.6 - - - +
95P LEU* 5.1 5.1 - - - +
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Residues in contact with ASP 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ASP* 5.2 2.9 - - - +
80P ARG* 2.6 48.1 + - - +
81P GLY* 3.7 10.5 - - - +
83P GLU* 1.3 80.0 - - - +
85P ILE* 1.3 61.2 + - + +
87P THR* 2.9 26.3 + - - +
88P MET* 3.0 24.6 - - + +
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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
----------------------------------------------------------
81P GLY 3.0 19.9 + - - +
82P ILE* 3.9 4.3 - - - +
84P ASP* 1.3 75.2 - - + +
86P ALA* 1.3 65.7 + - - +
88P MET* 3.2 19.8 + - + +
89P TYR* 3.1 31.0 + - + -
295P TYR* 4.1 8.5 - - + +
298P GLY 3.9 4.7 - - - +
299P ALA* 3.0 43.1 - - + +
302P MET* 3.6 36.3 - - + -
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Residues in contact with ALA 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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82P ILE 2.9 19.2 + - - +
83P GLU* 3.3 6.1 - - - +
85P ILE* 1.3 77.4 - - - +
87P THR* 1.3 58.2 + - + +
89P TYR* 2.8 22.3 + - - +
90P LYS 2.9 9.9 + - - -
91P TYR* 2.9 30.3 + - + +
93P ILE* 3.6 23.8 - - + -
302P MET* 4.4 9.9 - - + -
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Residues in contact with THR 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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99F ASP* 5.6 1.8 - - - +
104F LYS* 5.1 17.0 - - + +
83P GLU* 3.1 14.9 + - + +
84P ASP* 2.9 16.6 + - - +
86P ALA* 1.3 75.4 - - + +
88P MET* 1.3 70.2 + - - +
90P LYS* 2.8 22.2 + - - +
91P TYR 4.4 6.3 - - - +
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Residues in contact with MET 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ASP* 3.0 36.1 - - + +
85P ILE* 3.2 22.6 + - + +
87P THR* 1.3 84.5 + - - +
89P TYR* 1.3 63.5 + - + +
90P LYS* 3.3 1.2 + - - +
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Residues in contact with TYR 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ILE* 3.1 35.0 + - + +
86P ALA 2.8 5.4 + - - +
88P MET* 1.3 81.4 - - + +
90P LYS* 1.3 78.2 + - - +
91P TYR* 3.0 54.4 - + + -
299P ALA 3.9 2.8 + - - -
302P MET* 3.6 21.1 - - + -
303P ARG* 2.7 57.7 + - - +
306P THR* 3.8 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