Contacts of the helix formed by residues 74 - 91 (chain A) in PDB entry 1SQG
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 GLN 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A MET* 3.5 32.8 - - + +
71A THR 2.8 14.4 + - - +
73A LYS* 1.3 92.7 - - + +
75A ARG* 1.3 65.1 + - - +
76A THR 3.2 3.4 - - - -
77A VAL* 2.9 27.2 + - + +
111A ARG* 2.8 33.5 + - - +
113A GLN* 4.4 4.2 + - - -
114A LEU* 3.8 27.9 - - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.5 16.8 - - - +
20A GLU* 2.9 35.2 + - + +
59A ASP* 5.4 2.2 + - - -
69A PRO* 4.5 4.9 - - - +
70A MET 3.0 25.5 + - - -
71A THR* 3.6 18.3 + - - +
72A GLY 2.9 21.2 + - - +
73A LYS 3.4 1.4 + - - -
74A GLN* 1.3 77.0 - - - +
76A THR* 1.3 62.9 + - - +
78A HIS* 3.0 58.3 + - - +
79A TYR* 3.4 14.4 + - + -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 4.4 9.2 - - + -
13A GLN* 4.0 16.4 - - + +
16A GLU* 2.5 30.6 + - - +
73A LYS 5.1 1.3 + - - -
74A GLN 3.1 1.4 + - - -
75A ARG* 1.3 78.3 - - - +
77A VAL* 1.3 56.8 + - - +
79A TYR* 3.1 5.2 + - - +
80A LEU* 2.9 25.5 + - - +
109A ILE* 3.7 39.9 - - + -
111A ARG* 6.0 2.7 - - - -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.0 17.5 - - + -
74A GLN* 2.9 20.4 + - + +
76A THR* 1.3 73.2 - - - +
78A HIS* 1.3 65.1 + - - +
80A LEU* 3.2 2.8 + - - +
81A ILE* 2.9 28.4 + - + +
109A ILE* 3.9 20.4 - - + -
111A ARG* 4.0 24.5 - - + -
114A LEU* 4.2 16.4 - - + -
117A LEU* 4.4 6.5 - - + -
118A ILE* 3.9 28.3 - - + -
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 4.1 13.2 + - - -
62A ILE* 3.6 40.4 - - + +
63A ASN* 5.7 0.2 - - - -
66A MET* 5.8 0.4 - - - -
69A PRO* 4.2 9.8 - - + +
70A MET* 3.5 25.0 + - + +
74A GLN 3.6 1.8 + - - -
75A ARG* 3.0 52.6 + - - +
77A VAL* 1.3 79.3 - - - +
79A TYR* 1.3 78.5 + + - +
81A ILE* 3.2 7.7 + - - +
82A MET* 3.1 40.8 + - + +
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.5 25.6 - - - +
15A VAL* 3.7 28.0 - - + -
16A GLU* 3.7 17.5 - - + -
19A VAL* 3.3 28.8 - - + +
20A GLU* 2.7 41.5 + - + -
51A VAL* 5.3 0.8 - - + +
55A LEU* 4.6 2.7 - - + -
75A ARG* 3.4 27.9 + - + -
76A THR 3.1 6.9 + - - +
78A HIS* 1.3 80.6 + + - +
80A LEU* 1.3 60.1 + - - +
82A MET* 3.2 29.7 + - + +
83A VAL* 2.9 32.1 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.7 34.1 - - + +
9A SER* 4.2 2.7 - - - +
12A ALA* 3.6 10.2 - - + +
76A THR 2.9 14.4 + - - +
77A VAL* 3.6 9.6 - - - +
79A TYR* 1.3 77.3 - - - +
81A ILE* 1.3 61.8 + - - +
83A VAL* 3.2 3.5 + - + +
84A GLY 3.0 17.3 + - - -
102A THR* 3.2 46.7 - - + +
105A GLY* 3.6 23.3 - - - +
106A ALA 3.6 3.4 - - - +
109A ILE* 3.9 14.4 - - + -
118A ILE* 3.8 18.4 - - + -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.5 22.9 - - + -
66A MET* 4.0 20.6 - - + -
70A MET* 4.4 4.3 - - + -
77A VAL* 2.9 22.7 + - + +
78A HIS* 3.6 7.6 - - - +
80A LEU* 1.3 76.8 - - - +
82A MET* 1.3 56.4 + - - +
84A GLY* 3.0 3.8 + - - -
85A LEU* 2.9 28.4 + - + +
102A THR* 4.9 2.7 - - - -
117A LEU* 3.9 28.0 - - + -
118A ILE* 4.2 21.3 - - + -
121A VAL* 3.8 21.3 - - + -
122A LEU* 3.7 15.8 - - + +
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.5 4.3 - - + -
55A LEU* 3.2 30.1 - - + -
58A LEU* 3.6 22.2 - - + +
59A ASP* 3.7 28.7 - - - -
62A ILE* 3.7 17.7 - - + -
78A HIS* 3.1 31.5 + - + +
79A TYR* 3.2 35.0 + - + +
81A ILE* 1.3 76.4 - - - +
83A VAL* 1.3 57.1 + - - +
85A LEU* 3.2 9.2 + - + +
86A TYR* 2.8 29.8 + - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.8 27.8 - - + +
11A ALA* 4.1 8.3 - - + +
12A ALA* 3.8 26.0 - - - +
15A VAL* 5.3 0.4 - - + -
47A LEU* 4.3 16.6 - - + +
51A VAL* 3.9 24.5 - - + -
79A TYR 2.9 18.2 + - - +
80A LEU* 3.2 10.1 + - + +
82A MET* 1.3 73.8 - - - +
84A GLY* 1.3 62.7 + - - +
86A TYR* 3.3 3.6 + - - +
87A GLN* 3.0 38.7 + - - +
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 3.0 7.1 + - - -
81A ILE 3.0 8.2 + - - -
83A VAL* 1.3 73.8 - - - +
85A LEU* 1.3 65.5 + - - +
87A GLN* 3.1 15.1 + - - +
88A LEU* 3.2 15.9 + - - +
98A ALA* 5.2 1.8 - - - +
99A LEU* 6.4 0.2 - - - -
102A THR* 3.6 27.7 - - - +
122A LEU* 3.9 13.2 - - - -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.0 25.6 - - + +
61A LEU* 4.1 14.6 - - + -
62A ILE* 3.9 28.0 - - + -
65A LEU* 4.4 5.6 - - + -
81A ILE* 2.9 17.8 + - + +
82A MET* 3.2 9.8 + - - +
84A GLY* 1.3 75.0 - - - +
86A TYR* 1.3 63.2 + - - +
88A LEU* 3.1 7.3 + - - +
89A LEU* 3.0 33.0 + - + +
121A VAL* 5.9 0.2 - - + -
122A LEU* 3.8 15.0 - - + +
125A PHE* 3.5 46.0 - - + -
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 2.7 42.7 + - + -
47A LEU* 4.0 19.7 - - + -
50A GLY* 3.4 33.3 - - - -
51A VAL* 3.7 14.8 - - + -
53A ARG* 4.3 6.1 + - - -
54A THR* 3.5 22.2 - - + -
58A LEU* 4.1 7.7 - - + +
82A MET 2.8 16.7 + - - +
83A VAL 3.6 5.2 - - - +
84A GLY 3.2 0.2 - - - -
85A LEU* 1.3 75.5 - - - +
87A GLN* 1.3 59.3 + - - +
89A LEU 4.6 0.2 - - - +
90A TYR* 2.9 61.4 + + + +
91A THR* 3.9 12.3 + - + -
171A ARG* 5.1 0.7 - - - -
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 2.8 47.1 + - - +
47A LEU* 3.8 20.6 - - + -
83A VAL* 3.0 21.9 + - - +
84A GLY* 3.1 8.2 + - - +
86A TYR* 1.3 77.0 - - - +
88A LEU* 1.3 62.7 + - - +
91A THR* 2.8 41.0 + - + +
93A ILE* 4.0 13.5 - - + +
98A ALA* 3.8 26.0 + - + +
102A THR* 2.9 26.6 + - - -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLY 3.2 11.9 + - - +
85A LEU* 3.1 7.5 + - - +
87A GLN* 1.3 78.7 - - - +
89A LEU* 1.3 60.6 + - - +
91A THR 4.5 4.5 - - - +
93A ILE 5.6 0.7 - - - +
95A PRO* 3.7 37.9 - - + +
98A ALA* 4.3 6.5 - - + -
99A LEU* 3.8 30.3 - - + -
122A LEU* 4.4 12.6 - - + +
125A PHE* 3.7 33.7 - - + -
126A GLN* 4.0 14.4 - - + +
129A GLN* 4.5 13.3 + - - +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 4.0 24.2 - - - +
58A LEU* 3.7 29.8 - - + -
61A LEU* 3.8 20.0 - - + -
85A LEU 3.0 15.6 + - - +
88A LEU* 1.3 79.6 - - - +
90A TYR* 1.3 82.1 + - + +
91A THR 3.8 1.6 - - - -
125A PHE* 4.1 22.9 - - + -
129A GLN* 5.0 8.5 - - + +
133A LEU* 5.8 7.6 - - + -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 4.4 6.8 - - - +
54A THR* 3.7 23.2 - - + +
57A GLN* 2.5 37.6 + - - -
86A TYR* 2.9 48.5 + + + +
89A LEU* 1.3 108.6 - - + +
91A THR* 1.3 66.0 + - - +
144A LEU* 5.4 4.3 - - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.6 1.3 - - + -
46A GLU* 4.6 12.6 - - + +
47A LEU* 5.2 2.0 - - + -
86A TYR* 4.0 17.7 - - + -
87A GLN* 2.8 35.8 + - + +
88A LEU 4.5 5.4 - - - +
89A LEU 5.0 0.7 - - - -
90A TYR* 1.3 83.6 + - - +
92A ARG* 1.3 66.0 + - - +
93A ILE* 3.2 36.5 + - + +
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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