Contacts of the strand formed by residues 58 - 65 (chain B) in PDB entry 1SOT
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 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 3.8 12.1 - - - +
55B ALA 3.0 10.7 + - - +
56B PRO 3.2 3.2 - - - +
57B ALA* 1.3 78.6 - - - +
59B VAL* 1.3 64.6 + - - +
81B SER* 4.5 0.2 - - - -
82B GLY 3.4 9.9 - - - +
83B VAL* 4.6 3.1 - - + -
109B GLN* 4.7 5.7 + - - -
141B ILE* 4.8 1.6 - - + -
158B ILE* 3.7 38.8 - - + +
160B ASN* 3.3 36.5 - - + +
166B GLN* 3.6 9.6 - - - +
203B GLY* 4.5 7.0 - - - -
204B ALA* 3.9 24.7 - - + +
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Residues in contact with VAL 59 (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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56B PRO 5.0 1.3 - - - +
57B ALA 4.2 0.9 - - - +
58B VAL* 1.3 77.9 - - - +
60B ASN* 1.3 63.8 + - - +
61B VAL* 4.0 6.3 - - + -
81B SER* 3.1 7.6 - - - -
82B GLY* 2.8 51.4 + - - +
84B ILE* 3.7 23.6 - - + -
91B ILE* 4.5 7.9 - - + -
106B VAL* 3.9 19.1 - - + -
107B ALA 3.4 11.4 - - - +
108B LEU* 3.4 32.1 - - + +
160B ASN* 3.5 10.0 - - - +
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 1.3 76.0 - - - +
61B VAL* 1.3 61.3 + - - +
62B TYR* 3.5 34.4 + - + +
80B GLY 3.5 5.6 - - - +
105B ILE 4.0 0.3 - - - +
106B VAL* 3.4 4.7 - - - -
107B ALA* 3.0 42.3 + - - +
108B LEU 5.1 2.4 + - - -
109B GLN* 4.9 3.4 - - - +
160B ASN* 2.4 49.8 + - - +
161B PRO 3.8 11.3 - - - +
162B TYR* 4.1 3.2 + - + -
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Residues in contact with VAL 61 (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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59B VAL* 4.0 8.1 - - + -
60B ASN* 1.3 78.5 - - - +
62B TYR* 1.3 66.9 + - - +
63B ASN 4.2 0.2 + - - -
78B THR 4.2 0.2 - - - +
79B LEU* 3.5 5.7 - - - +
80B GLY 2.7 40.7 + - - +
81B SER 3.7 23.8 - - - +
82B GLY* 3.8 9.4 - - - +
91B ILE* 5.2 0.2 - - + -
93B THR* 4.0 7.4 - - - +
97B VAL* 4.1 11.3 - - + +
98B ILE* 4.1 14.1 - - + -
104B ILE* 4.0 23.3 - - + -
105B ILE 3.6 4.5 - - - +
106B VAL* 4.1 7.9 - - + -
130B LEU* 4.1 10.3 - - + -
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Residues in contact with TYR 62 (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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60B ASN* 3.5 30.3 + - + +
61B VAL* 1.3 80.2 - - - +
63B ASN* 1.3 60.1 + - - +
64B ARG* 3.9 4.4 + - + -
76B ILE* 4.4 26.2 - - + -
78B THR 4.0 2.2 - - - -
79B LEU* 4.1 14.1 - - + -
103B GLN 3.5 2.6 - - - +
104B ILE* 3.5 7.0 - - - +
105B ILE* 2.8 68.9 + - + +
107B ALA* 3.7 27.1 - - + +
162B TYR* 4.0 42.5 - + + -
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Residues in contact with ASN 63 (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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61B VAL* 4.2 0.8 + - - +
62B TYR* 1.3 70.7 - - - +
64B ARG* 1.3 72.7 + - - +
76B ILE* 4.0 0.2 - - - -
77B ARG* 2.8 33.4 + - - +
78B THR* 2.9 28.8 + - - +
96B HIS 5.3 0.5 - - - +
97B VAL* 3.1 27.4 - - + +
98B ILE* 3.8 2.9 - - + -
99B ASN 3.0 21.7 - - - +
100B ASP 4.2 1.8 + - - -
101B ALA* 2.9 38.3 - - + +
103B GLN 4.2 2.2 - - - -
104B ILE* 5.1 1.3 - - - +
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Residues in contact with ARG 64 (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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62B TYR 4.3 7.2 - - - +
63B ASN* 1.3 84.3 - - - +
65B GLY* 1.2 63.9 + - - +
74B LEU* 1.6 79.0 + - + +
75B GLU 3.6 11.0 - - - +
76B ILE* 3.8 25.7 - - + +
77B ARG* 3.6 6.5 - - - +
102B ASP* 2.7 29.3 + - - +
103B GLN* 2.9 32.4 + - - +
105B ILE* 4.8 13.7 - - - +
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Residues in contact with GLY 65 (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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64B ARG* 1.2 77.0 - - - +
66B LEU* 1.3 56.0 + - - -
67B ASN 3.4 0.9 - - - -
68B THR* 2.6 25.5 + - - -
73B GLN 3.1 15.2 - - - +
74B LEU* 3.3 5.1 - - - -
75B GLU 3.1 3.6 + - - -
77B ARG* 3.2 18.7 - - - +
102B ASP* 2.1 23.1 - - - -
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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