Contacts of the strand formed by residues 79 - 87 (chain B) in PDB entry 3SHD
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 PHE 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PRO* 5.0 1.1 - - - -
5B HIS* 3.5 18.4 - + + -
7B THR* 3.7 23.3 - - + +
37B HIS* 3.6 28.7 - + - -
69B HIS 4.4 0.2 - - - -
70B GLN* 3.3 1.6 - - - +
71B TRP* 2.8 70.7 + + + +
72B ILE 4.1 0.2 - - - -
73B ALA* 4.6 2.9 - - + -
77B THR* 3.4 40.8 - - + -
78B PRO* 1.3 72.8 - - - +
80B LEU* 1.3 73.5 + - - +
81B ARG* 4.0 5.8 - - + +
158B SO4 4.5 13.0 - - - -
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Residues in contact with LEU 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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4B PRO* 4.1 15.7 - - + -
5B HIS 2.7 13.6 + - - +
6B VAL* 3.2 15.1 - - + +
7B THR* 2.8 30.6 + - - +
68B MET* 3.9 14.4 - - + -
69B HIS 3.7 3.6 - - - -
70B GLN* 3.5 34.1 - - + +
79B PHE* 1.3 83.7 - - - +
81B ARG* 1.3 54.1 + - - +
82B PHE* 4.1 9.4 - - + -
6L VAL* 3.8 32.8 - - + -
38L LEU* 4.7 2.9 - - + -
44L LEU* 4.9 2.9 - - + -
80L LEU* 5.3 0.9 - - + -
82L PHE* 4.2 19.7 - - + -
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Residues in contact with ARG 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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7B THR* 3.3 19.1 - - - +
9B ALA* 3.6 30.2 - - + +
32B ASN* 3.5 17.2 + - - -
33B GLN* 2.8 26.7 + - - +
67B ARG 4.2 0.2 - - - +
68B MET* 3.4 2.9 - - - +
69B HIS* 2.9 49.6 + - + +
71B TRP* 6.1 0.4 - - - -
79B PHE* 5.1 5.8 - - + -
80B LEU* 1.3 71.7 - - - +
82B PHE* 1.3 62.7 + - - +
83B LEU* 3.8 6.0 + - - +
120B SER* 5.2 2.1 + - - -
122B LEU* 3.5 37.4 + - + +
123B VAL* 4.5 2.2 - - - +
126B SER* 2.9 22.6 + - - -
158B SO4 3.1 26.3 + - - +
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Residues in contact with PHE 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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6B VAL* 4.0 18.8 - - + -
7B THR 2.9 18.6 + - - +
8B VAL* 3.3 4.3 - - + -
9B ALA* 3.0 27.2 + - - +
44B LEU* 3.7 27.6 - - + -
65B PHE* 3.6 22.4 - + + -
67B ARG 3.8 3.8 - - - -
68B MET* 3.8 30.1 - - + -
80B LEU* 4.1 9.9 - - + -
81B ARG* 1.3 76.7 - - - +
83B LEU* 1.3 59.7 + - - +
84B PHE* 3.7 19.5 - - + -
141B ILE* 3.7 20.9 - - + -
68L MET* 3.9 12.1 - - - -
80L LEU* 4.7 6.1 - - + -
82L PHE* 3.8 16.2 - + - -
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Residues in contact with LEU 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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9B ALA* 3.5 28.0 - - + +
10B CYS 4.4 0.9 - - - +
11B VAL* 3.7 22.4 - - + -
33B GLN* 4.8 1.8 - - - +
65B PHE* 3.3 11.1 - - - -
66B ILE* 2.8 51.2 + - + -
67B ARG* 2.7 20.3 + - + +
69B HIS* 4.5 12.6 - - + +
81B ARG* 3.8 6.0 + - - +
82B PHE* 1.3 70.5 - - - +
84B PHE* 1.3 57.4 + - - +
126B SER* 3.4 47.3 - - - +
129B CYS* 4.4 4.9 - - + -
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Residues in contact with PHE 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 VAL* 4.1 9.6 - - + -
9B ALA 3.0 18.7 + - - +
10B CYS* 4.1 11.9 - - - -
11B VAL* 2.9 29.8 + - - +
44B LEU* 4.2 11.7 - - + -
45B VAL* 4.2 9.0 - - + -
48B ALA* 3.8 22.4 - - + -
62B PRO* 3.9 14.6 - - + -
64B HIS 3.2 10.8 - - - +
65B PHE* 4.0 11.7 - + - -
66B ILE* 4.2 3.1 - - - -
82B PHE* 3.7 31.0 - - + -
83B LEU* 1.3 73.1 - - - +
85B ALA* 1.3 61.4 + - - +
138B LEU* 3.7 31.9 - - + -
141B ILE* 3.9 25.6 - - + -
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Residues in contact with ALA 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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11B VAL 3.7 5.8 - - - +
63B GLN* 2.8 32.1 + - - +
64B HIS* 2.7 27.8 + - + +
66B ILE* 3.8 24.2 - - + -
84B PHE* 1.3 75.6 - - - +
86B ILE* 1.3 58.2 + - - +
87B GLU* 5.6 2.5 - - + +
130B TYR* 4.5 15.3 - - + -
135B ARG* 5.7 4.5 - - + +
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Residues in contact with ILE 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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10B CYS* 4.4 20.2 - - + -
11B VAL 3.1 11.3 + - - +
12B VAL* 3.6 18.9 - - + +
13B HIS* 3.0 26.7 + - - +
52B LEU* 4.8 7.4 - - + -
60B ALA* 4.2 20.0 - - + +
61B GLN 3.6 24.2 - - - +
62B PRO* 3.9 13.7 - - + -
63B GLN* 3.5 13.5 - - - +
85B ALA* 1.3 80.3 - - - +
87B GLU* 1.3 64.1 + - - +
88B LEU* 3.5 28.3 - - + -
130B TYR* 6.1 0.6 - - - -
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Residues in contact with GLU 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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13B HIS* 2.8 32.2 - - - +
63B GLN* 2.7 35.3 - - - +
85B ALA* 5.6 2.6 - - + +
86B ILE* 1.3 76.1 - - - +
88B LEU* 1.3 69.8 + - - +
89B GLU* 5.2 4.9 - - - +
130B TYR* 2.5 35.0 + - - -
135B ARG* 5.2 5.2 + - - +
125C GLU* 4.4 5.8 - - - +
128C ARG* 3.4 44.1 + - - +
144G PHE* 6.5 0.7 - - + -
145G ASN* 5.5 1.9 - - - +
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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