Contacts of the helix formed by residues 77 - 90 (chain A) in PDB entry 1SXQ
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLY 4.5 5.9 + - - -
70A ASN 4.8 5.3 + - - +
71A PHE* 3.7 20.2 - - + -
72A PHE* 6.0 2.6 - - - +
75A LYS 3.6 2.1 + - - +
76A PRO* 1.3 73.8 - - - +
78A LEU* 1.3 63.6 + - - +
79A ALA* 2.9 23.1 + - - +
80A ILE* 3.2 26.3 + - + +
81A LEU* 3.0 28.3 + - - +
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Residues in contact with LEU 78 (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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42A LEU* 4.0 14.8 - - + -
76A PRO* 4.0 7.4 + - + -
77A ASN* 1.3 71.3 + - - +
79A ALA* 1.3 60.5 + - - +
81A LEU* 4.4 5.6 - - + -
82A SER* 2.8 45.0 + - - +
121A TYR* 3.9 21.1 - - - +
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Residues in contact with ALA 79 (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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7A ASN 4.6 1.4 - - - +
8A MET 3.7 4.0 - - - +
9A GLY* 3.7 22.7 - - - +
10A ASN* 3.8 6.3 - - - +
11A ASN* 3.9 15.3 - - + +
42A LEU* 4.1 20.3 - - + +
51A PHE* 4.9 2.7 - - - -
77A ASN* 2.9 12.5 + - - +
78A LEU* 1.3 78.2 - - - +
80A ILE* 1.3 61.9 + - - +
82A SER* 4.6 0.3 - - - -
83A ALA* 3.2 23.6 + - - +
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Residues in contact with ILE 80 (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 MET 3.4 7.2 - - - +
9A GLY* 3.8 20.0 - - - +
68A SER 4.1 2.5 - - - +
69A ILE* 3.4 56.8 - - + +
70A ASN 3.7 12.8 - - - +
71A PHE* 3.9 18.4 - - + -
77A ASN* 3.2 30.4 + - + +
79A ALA* 1.3 75.6 - - - +
81A LEU* 1.3 60.2 + - - +
83A ALA* 3.4 1.7 + - - +
84A GLN* 3.0 32.8 + - + +
108A SER* 4.5 9.4 - - - -
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Residues in contact with LEU 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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71A PHE* 3.7 23.3 - - + -
76A PRO* 3.9 7.4 - - + -
77A ASN 3.0 33.8 + - - +
78A LEU* 4.2 5.2 - - + +
80A ILE* 1.3 76.4 - - - +
82A SER* 1.3 57.7 + - - +
84A GLN* 3.4 0.6 + - - -
85A LYS* 2.9 36.1 + - - +
108A SER* 4.6 2.0 - - - +
112A VAL* 4.0 7.0 - - + -
117A TRP* 3.8 18.8 - - + -
121A TYR* 3.4 33.4 - - + +
126A LEU* 3.6 33.0 - - + +
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Residues in contact with SER 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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42A LEU* 3.9 8.2 - - - +
51A PHE* 3.6 32.9 - - - +
78A LEU* 2.8 33.7 + - - +
81A LEU* 1.3 73.3 - - - +
83A ALA* 1.3 62.7 + - - +
85A LYS* 3.5 9.5 + - - +
86A PHE* 3.0 23.2 + - - +
121A TYR* 5.5 0.7 + - - -
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Residues in contact with ALA 83 (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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6A ILE* 3.9 6.1 - - + +
7A ASN 3.7 16.4 - - - +
8A MET* 3.5 23.3 - - + +
51A PHE* 3.8 16.7 - - + -
79A ALA 3.2 20.4 + - - +
81A LEU 3.3 0.6 - - - -
82A SER* 1.3 79.9 - - - +
84A GLN* 1.3 57.3 + - - +
86A PHE* 3.2 4.9 - - - +
87A MET* 2.9 32.6 + - - +
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Residues in contact with GLN 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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8A MET* 3.5 30.1 - - + +
69A ILE* 4.1 5.1 - - - +
80A ILE* 3.0 22.8 + - + +
81A LEU 4.2 2.7 - - - +
83A ALA* 1.3 74.8 - - - +
85A LYS* 1.3 60.8 + - - +
87A MET* 3.6 6.8 - - - +
88A ALA* 2.8 31.4 + - - +
106A SER 3.0 20.8 - - - +
107A GLN* 3.9 1.6 - - - +
108A SER* 2.6 50.9 + - - +
126A LEU* 4.0 14.3 + - + +
128A ILE* 3.7 21.7 - - + +
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Residues in contact with LYS 85 (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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81A LEU 2.9 20.5 + - - +
82A SER* 3.8 8.3 - - - +
84A GLN* 1.3 76.2 - - - +
86A PHE* 1.3 63.2 + - - +
88A ALA* 3.3 1.9 + - - +
89A LYS* 3.0 25.1 + - - +
121A TYR* 3.4 30.0 - - + -
125A GLU* 3.4 38.6 + - - +
126A LEU* 3.5 15.5 - - + -
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Residues in contact with PHE 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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4A ALA* 4.9 1.6 - - + -
6A ILE* 4.0 19.3 - - + -
40A ILE* 3.8 24.0 - - + -
51A PHE* 3.6 36.3 - + + -
54A VAL* 3.8 31.4 - - + -
56A VAL* 3.5 56.9 - - + +
59A TYR* 5.0 2.5 - + - -
62A LEU* 4.3 8.1 - - + -
82A SER 3.0 14.4 + - - +
83A ALA 3.2 9.9 - - - +
85A LYS* 1.3 77.3 - - - +
87A MET* 1.3 60.7 + - - +
89A LYS* 3.3 7.7 + - + +
90A TYR 3.3 14.7 + - - -
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Residues in contact with MET 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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6A ILE* 3.9 14.8 - - + -
8A MET* 3.8 29.6 - - - +
62A LEU* 4.1 11.9 - - + -
64A VAL* 3.9 28.3 - - + -
83A ALA 2.9 21.9 + - - +
84A GLN* 3.6 6.1 - - - +
86A PHE* 1.3 77.1 - - - +
88A ALA* 1.3 61.9 + - - +
90A TYR* 3.1 20.6 + - - +
94A ILE* 3.8 28.8 - - + +
96A TYR* 5.0 1.1 - - + -
105A PHE* 3.7 29.4 - - + -
128A ILE* 3.7 18.4 - - + +
130A SER* 4.9 0.7 + - - -
132A ILE* 5.2 1.1 - - + -
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Residues in contact with ALA 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 GLN 2.8 21.5 + - - +
85A LYS 3.7 0.4 - - - +
87A MET* 1.3 73.4 - - - +
89A LYS* 1.3 61.3 + - - +
90A TYR 3.5 5.0 + - - +
91A LYS* 5.0 7.4 + - - -
124A GLU 4.4 5.6 - - - +
125A GLU 3.3 24.0 - - - +
126A LEU 3.9 7.4 - - - +
127A LEU 3.7 20.3 - - - +
128A ILE* 3.9 11.8 - - + +
129A LYS* 5.1 4.3 + - - +
130A SER 5.9 0.3 + - - -
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Residues in contact with LYS 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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55A ASP* 5.5 2.7 + - - +
56A VAL* 3.9 14.1 - - + -
57A ASN* 3.0 25.4 + - - +
85A LYS 3.0 16.9 + - - +
86A PHE* 3.7 7.4 - - + +
87A MET 3.2 0.4 - - - -
88A ALA* 1.3 75.8 - - - +
90A TYR* 1.3 62.6 + - - +
91A LYS* 3.5 13.4 + - - +
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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
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56A VAL* 3.5 35.2 - - + -
57A ASN* 3.5 17.3 - - - -
59A TYR* 3.4 13.4 + - + -
60A ASP 3.2 32.9 + - - -
61A ARG* 3.3 3.5 + - - -
62A LEU* 3.6 35.7 - - + -
86A PHE 3.3 3.0 + - - +
87A MET 3.1 17.4 + - - +
88A ALA 3.8 5.2 - - - +
89A LYS* 1.3 79.7 - - - +
91A LYS* 1.3 58.4 + - - +
92A SER* 3.3 40.0 - - - -
93A LYS 3.4 21.6 + - - -
94A ILE* 3.9 8.5 - - + -
130A SER* 2.7 21.8 + - - -
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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