Contacts of the helix formed by residues 77 - 89 (chain B) in PDB entry 1SXP
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY 4.2 9.7 + - - -
70B ASN 4.9 2.8 + - - -
71B PHE* 3.7 14.4 - - + -
72B PHE* 5.6 4.9 - - - +
75B LYS 3.3 4.4 + - - +
76B PRO* 1.3 72.5 - - - +
78B LEU* 1.3 61.5 + - - +
79B ALA* 2.7 34.8 + - - +
80B ILE* 3.3 33.7 + - + +
81B LEU* 3.1 26.1 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.4 19.9 - - + +
76B PRO* 3.9 19.3 - - + +
77B ASN* 1.3 71.3 + - - +
79B ALA* 1.3 60.3 + - - +
81B LEU* 4.5 4.3 - - + +
82B SER* 2.9 45.3 + - - +
121B TYR* 3.8 21.1 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN 4.5 1.6 - - - +
8B MET 3.3 5.1 - - - +
9B GLY* 3.7 23.3 - - - +
10B ASN* 3.7 17.0 - - - +
11B ASN* 3.9 4.3 - - + +
42B LEU* 4.1 21.2 - - + +
51B PHE* 4.9 2.5 - - - -
77B ASN* 2.7 21.9 + - - +
78B LEU* 1.3 75.2 - - - +
80B ILE* 1.3 58.9 + - - +
82B SER* 4.7 0.2 - - - -
83B ALA* 3.2 22.9 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 3.4 8.7 - - + +
9B GLY* 3.7 19.3 - - - +
68B SER 3.7 9.0 - - - +
69B ILE* 3.7 29.2 - - + +
70B ASN 3.4 25.1 - - - +
71B PHE* 4.0 22.0 - - + -
77B ASN* 3.3 30.6 + - + +
78B LEU 3.2 0.2 - - - -
79B ALA* 1.3 74.7 - - - +
81B LEU* 1.3 68.2 + - - +
83B ALA* 3.3 2.4 + - - +
84B GLN* 3.0 27.3 + - + +
108B SER* 4.3 14.8 - - - -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 4.0 9.2 - - + -
76B PRO* 4.1 5.8 - - + -
77B ASN 3.1 29.2 + - - +
78B LEU* 4.3 3.6 - - + +
80B ILE* 1.3 79.9 - - - +
82B SER* 1.3 57.6 + - - +
84B GLN* 3.2 2.3 + - - -
85B LYS* 2.8 30.8 + - - +
108B SER* 4.5 2.9 - - - +
112B VAL* 4.0 17.7 - - + -
117B TRP* 3.9 14.8 - - + -
121B TYR* 3.3 46.2 - - + +
126B LEU* 3.7 37.8 - - + +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.6 11.4 - - - +
51B PHE* 3.6 29.1 - - - +
78B LEU* 2.9 36.0 + - - +
81B LEU* 1.3 72.4 - - - +
83B ALA* 1.3 60.8 + - - +
85B LYS* 3.4 11.0 + - - +
86B PHE* 3.1 22.9 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.0 9.2 - - + +
7B ASN 3.9 12.8 - - - +
8B MET* 3.3 24.2 - - + +
51B PHE* 3.7 16.5 - - + -
79B ALA 3.2 21.2 + - - +
80B ILE 3.3 0.8 + - - +
81B LEU 3.2 0.4 - - - -
82B SER* 1.3 78.9 - - - +
84B GLN* 1.3 58.1 + - - +
86B PHE* 3.1 6.1 + - - +
87B MET* 2.9 31.1 + - - +
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 3.8 25.2 - - + +
69B ILE* 3.8 8.3 - - - +
80B ILE* 3.0 21.0 + - + +
81B LEU 3.9 2.7 - - - +
83B ALA* 1.3 73.4 - - - +
85B LYS* 1.3 61.6 + - - +
87B MET* 3.7 7.4 - - - +
88B ALA* 2.8 32.2 + - - +
106B SER 3.0 22.5 - - - +
108B SER* 2.8 45.3 + - - +
126B LEU* 3.8 15.0 + - + +
128B ILE* 3.5 24.6 - - + +
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU 2.8 16.7 + - - +
82B SER* 3.5 11.0 - - - +
84B GLN* 1.3 76.8 - - - +
86B PHE* 1.3 62.9 + - - +
88B ALA* 3.3 3.6 + - - +
89B LYS* 3.3 27.7 + - + +
121B TYR* 4.9 7.0 - - + -
125B GLU* 2.9 58.4 + - + +
126B LEU* 4.2 5.3 - - + +
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 5.2 1.1 - - + -
6B ILE* 4.3 11.4 - - + -
40B ILE* 4.0 22.7 - - + -
51B PHE* 3.7 34.5 - + + -
54B VAL* 3.6 32.1 - - + -
56B VAL* 3.4 61.5 - - + +
59B TYR* 4.8 2.2 - + - -
62B LEU* 4.3 13.7 - - + -
82B SER 3.1 11.0 + - - +
83B ALA 3.2 8.7 - - - +
85B LYS* 1.3 80.2 - - - +
87B MET* 1.3 63.6 + - - +
89B LYS* 3.3 14.8 + - + +
90B TYR 3.5 6.8 + - - -
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Residues in contact with MET 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.1 13.7 - - + -
8B MET* 3.9 24.9 - - - +
62B LEU* 4.3 12.6 - - + -
64B VAL* 3.6 34.1 - - + -
83B ALA 2.9 18.1 + - - +
84B GLN* 3.2 11.6 + - - +
86B PHE* 1.3 75.7 - - - +
88B ALA* 1.3 64.7 + - - +
90B TYR* 2.9 22.0 + - - +
94B ILE* 3.8 29.1 - - + +
96B TYR* 5.2 1.1 - - + -
105B PHE* 4.2 23.8 - - + -
128B ILE* 4.0 17.2 - - + +
130B SER* 4.7 0.7 + - - -
132B ILE* 5.0 0.9 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLN 2.8 20.6 + - - +
85B LYS 3.6 2.2 - - - +
86B PHE 3.3 0.2 - - - -
87B MET* 1.3 73.9 - - - +
89B LYS* 1.3 74.1 + - - +
90B TYR 3.5 4.3 + - - +
91B LYS* 4.3 10.6 + - - -
124B GLU 4.6 0.4 - - - +
125B GLU 3.4 22.4 - - - +
126B LEU 4.0 6.1 - - - +
127B LEU 3.6 22.6 - - - +
128B ILE* 4.0 10.4 - - - +
129B LYS 5.2 3.0 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 6.1 0.4 - - - +
56B VAL* 3.6 11.4 - - + -
57B ASN* 3.0 21.1 + - - +
85B LYS* 3.3 16.2 + - + +
86B PHE* 3.3 11.8 + - + +
87B MET 3.1 1.2 - - - -
88B ALA* 1.3 89.0 + - + +
90B TYR* 1.3 62.2 + - - +
91B LYS* 3.5 10.5 + - - +
124B GLU* 3.2 40.4 + - - +
125B GLU* 4.7 4.8 - - - +
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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