Contacts of the helix formed by residues 78 - 88 (chain B) in PDB entry 1S9V
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 VAL 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.3 5.6 - - + -
15B CYS* 4.2 12.1 - - - -
26B LEU* 4.6 2.2 - - + -
74B ALA* 2.6 29.9 + - + +
77B ARG* 1.3 82.1 - - + +
79B CYS* 1.3 61.3 + - - +
80B ARG 3.7 0.4 - - - -
81B HIS* 3.3 2.6 + - - +
82B ASN* 2.9 40.0 + - - +
4C PHE* 3.2 26.0 - - + +
5C PRO 4.0 17.3 - - - +
6C GLN* 4.0 26.9 - - + +
7C PRO* 6.1 0.4 - - + -
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Residues in contact with CYS 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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9A TYR* 4.9 1.6 - - - -
15B CYS* 2.0 52.5 - - + -
17B PHE* 3.4 14.1 - - + -
24B VAL* 3.6 17.7 - - + -
26B LEU* 3.7 34.8 - - - -
74B ALA 3.4 2.2 + - - -
75B VAL* 3.1 11.2 - - - +
78B VAL* 1.3 80.5 - - - +
80B ARG* 1.3 64.7 + - - +
81B HIS 3.1 0.3 + - - -
82B ASN* 3.2 1.2 + - - +
83B TYR* 3.0 18.7 + - - +
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Residues in contact with ARG 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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17B PHE* 4.7 1.6 - - - -
21B THR* 3.5 34.1 + - + +
22B GLU 4.3 9.1 + - - -
24B VAL* 3.8 28.0 + - + +
75B VAL* 2.9 31.9 + - - +
76B ASP* 2.8 45.2 + - + +
78B VAL 3.7 0.2 - - - -
79B CYS* 1.3 72.8 - - - +
81B HIS* 1.3 63.2 + - - +
83B TYR* 3.6 10.8 + - - +
84B GLN* 3.4 21.9 + - - +
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Residues in contact with HIS 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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76B ASP 3.3 10.3 + - - +
77B ARG* 2.9 24.9 - - - +
78B VAL 3.4 0.7 - - - +
79B CYS 3.0 0.6 - - - -
80B ARG* 1.3 74.7 - - - +
82B ASN* 1.3 86.1 - - - +
84B GLN* 3.1 24.3 + - + +
85B LEU* 3.7 17.2 + - + +
2C GLN 3.1 20.8 + - - -
4C PHE* 3.4 35.6 - + - -
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Residues in contact with ASN 82 (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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9A TYR* 3.3 47.5 - - + -
504A EDO 4.1 4.0 + - - +
78B VAL* 2.9 22.3 + - - +
79B CYS 4.0 0.2 - - - +
81B HIS* 1.3 78.9 - - - +
83B TYR* 1.3 62.6 + - - +
85B LEU* 3.2 9.9 + - - +
86B GLU* 3.0 24.1 + - - +
3C PRO* 3.1 13.9 - - - +
4C PHE 2.7 48.8 + - - +
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Residues in contact with TYR 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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5A HIS* 3.9 21.5 + + - -
9A TYR* 4.7 1.7 + - - -
26A PHE* 5.0 2.9 - + - -
17B PHE* 3.3 52.3 - + + -
20B GLY* 4.0 24.0 + - - -
21B THR* 3.5 24.7 - - + -
79B CYS 3.0 16.6 + - - +
80B ARG 3.8 6.7 - - - +
81B HIS 3.2 0.4 - - - -
82B ASN* 1.3 76.4 - - - +
84B GLN* 1.3 57.5 + - - +
86B GLU* 3.3 7.7 + - + +
87B LEU* 2.9 56.5 + - + +
91B LEU* 3.6 21.3 - - + +
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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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21B THR* 4.5 15.6 + - - +
80B ARG* 3.4 18.3 - - - +
81B HIS* 3.1 12.2 + - - +
83B TYR* 1.3 75.6 - - - +
85B LEU* 1.3 69.3 + - + +
87B LEU* 3.3 29.2 + - - +
88B ARG* 3.4 20.1 + - - +
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Residues in contact with LEU 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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51A PHE* 3.6 23.6 - - + -
504A EDO 4.1 9.0 - - - +
81B HIS* 4.0 22.9 - - + +
82B ASN* 3.2 8.7 + - - +
84B GLN* 1.3 80.3 - - + +
86B GLU* 1.3 56.3 + - - +
88B ARG* 3.3 37.3 + - - +
89B THR* 2.8 27.5 + - - +
1C LEU* 4.6 6.7 - - - -
2C GLN 3.5 14.8 - - - +
3C PRO* 3.5 38.8 - - + -
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Residues in contact with GLU 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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9A TYR* 2.7 25.5 + - - -
26A PHE* 3.5 29.1 - - + -
31A GLN* 2.7 25.6 + - - -
48A LEU* 4.7 0.3 - - - +
504A EDO 3.6 14.6 + - - -
82B ASN 3.0 9.0 + - - +
83B TYR* 3.4 14.1 - - + +
84B GLN 3.1 0.2 - - - -
85B LEU* 1.3 73.6 - - - +
87B LEU* 1.3 64.2 + - - +
88B ARG 3.0 2.0 - - - -
89B THR* 3.0 14.4 + - - -
90B THR* 2.5 34.7 + - - -
91B LEU* 3.0 28.7 + - + -
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Residues in contact with LEU 87 (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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21B THR* 5.7 0.9 - - + -
83B TYR* 2.9 48.0 + - + +
84B GLN* 3.3 28.7 + - - +
86B GLU* 1.3 77.6 - - - +
88B ARG* 1.3 60.1 + - + +
89B THR 3.3 0.2 - - - -
91B LEU* 3.8 16.7 - - + +
92B GLN* 2.9 28.3 - - - +
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Residues in contact with ARG 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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47A VAL* 5.1 1.9 - - - +
50A GLN* 4.9 11.4 + - - +
51A PHE* 3.6 18.1 - - - -
84B GLN* 3.6 15.6 + - - +
85B LEU* 3.3 35.4 + - - +
86B GLU 3.0 1.2 - - - -
87B LEU* 1.3 80.2 - - + +
89B THR* 1.3 66.7 + - + +
92B GLN* 3.7 22.1 + - - +
1C LEU* 4.6 6.9 - - - +
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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