Contacts of the strand formed by residues 75 - 84 (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 GLU 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B ARG* 3.8 2.2 - - - -
65B GLY 3.1 8.7 + - - -
68B THR* 2.9 36.1 + - + +
69B ASN* 2.7 45.4 + - - +
73B GLN 2.7 3.8 + - - -
74B LEU* 1.3 71.8 - - - +
76B ILE* 1.3 75.9 + - + +
77B ARG* 2.9 18.7 + - - +
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Residues in contact with ILE 76 (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* 4.4 27.8 - - + -
63B ASN 4.7 0.9 - - - +
64B ARG* 3.8 23.1 - - + +
68B THR* 4.9 0.2 - - - +
74B LEU 3.9 2.5 + - - +
75B GLU* 1.3 78.1 - - - +
77B ARG* 1.3 63.4 + - - +
78B THR 4.7 4.0 - - - +
79B LEU* 4.3 30.1 - - + -
162B TYR* 5.2 11.9 - - + -
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Residues in contact with ARG 77 (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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63B ASN* 2.8 18.6 + - - +
64B ARG 3.6 2.7 - - - -
65B GLY* 3.2 14.1 - - - +
67B ASN 5.7 1.6 - - - +
68B THR* 3.2 35.4 + - + +
75B GLU 2.9 12.6 + - - +
76B ILE* 1.3 74.5 - - - +
78B THR* 0.9 69.2 + - - +
79B LEU* 4.1 9.5 + - - +
99B ASN 4.9 1.0 + - - -
100B ASP* 3.2 42.4 + - - +
102B ASP* 3.3 18.2 + - - -
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Residues in contact with THR 78 (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* 4.0 0.9 - - - -
63B ASN* 2.9 47.5 + - - +
76B ILE* 4.7 1.1 - - - +
77B ARG* 0.9 86.9 + - - +
79B LEU* 1.3 75.4 + - - +
96B HIS* 4.3 9.9 - - + +
97B VAL* 3.9 21.2 - - + +
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Residues in contact with LEU 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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61B VAL 3.5 8.7 - - - +
62B TYR* 4.1 11.0 - - + +
76B ILE* 4.3 16.4 - - + -
77B ARG 4.3 9.6 - - - +
78B THR* 1.3 86.9 - - - +
80B GLY* 1.3 60.7 + - - +
97B VAL* 3.5 15.6 - - - +
161B PRO* 6.2 0.9 - - + -
162B TYR* 3.3 53.8 - - + +
198B HIS 5.3 1.9 - - - +
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Residues in contact with GLY 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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60B ASN* 3.5 6.4 - - - +
61B VAL* 2.7 35.8 + - - +
79B LEU* 1.3 80.4 - - - +
81B SER* 1.3 61.0 + - - -
97B VAL* 3.8 15.5 - - - -
160B ASN 3.7 5.8 - - - +
161B PRO* 5.4 2.1 - - - +
198B HIS 4.9 8.5 - - - -
201B SER 4.4 2.7 - - - -
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Residues in contact with SER 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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58B VAL* 4.5 1.8 - - - -
59B VAL 3.1 8.7 - - - -
61B VAL* 3.7 4.0 - - - -
80B GLY* 1.3 73.0 - - - -
82B GLY* 1.3 55.4 + - - +
93B THR* 2.6 27.1 + - - -
160B ASN 2.7 35.4 + - - -
198B HIS 5.5 0.2 + - - -
199B GLY 3.5 10.4 + - - -
200B ASN 4.0 0.9 - - - -
201B SER 3.3 18.6 + - - +
202B GLY* 3.3 10.8 - - - +
203B GLY* 3.5 18.6 - - - -
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Residues in contact with GLY 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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58B VAL* 3.4 6.1 - - - +
59B VAL* 2.8 37.8 + - - +
61B VAL* 3.8 8.2 - - - +
81B SER* 1.3 76.2 - - - +
83B VAL* 1.3 67.2 + - - +
91B ILE* 4.2 1.6 - - - -
92B ILE 3.1 13.7 - - - -
93B THR* 4.0 5.2 - - - -
202B GLY 3.3 3.6 - - - -
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Residues in contact with VAL 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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57B ALA 3.6 6.5 - - - +
58B VAL* 4.6 2.2 - - + -
82B GLY* 1.3 80.1 - - - +
84B ILE* 1.3 63.5 + - - +
85B MSE 3.3 20.6 + - - +
91B ILE* 3.3 5.0 - - - +
92B ILE 2.7 37.9 + - - +
141B ILE* 3.7 36.8 - - + -
202B GLY 3.6 4.3 - - - +
203B GLY* 3.5 31.4 - - - +
204B ALA* 3.6 11.7 - - + +
212B LEU* 4.9 1.1 - - + -
215B ILE* 4.0 12.6 - - + -
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Residues in contact with ILE 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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57B ALA* 3.0 13.1 + - + +
59B VAL* 3.7 26.0 - - + -
83B VAL* 1.3 70.1 - - - +
85B MSE 1.3 60.9 + - - +
86B ASP 3.7 20.2 - - - +
89B GLY* 5.2 0.2 - - - -
90B TYR 3.7 7.4 - - - +
91B ILE* 3.9 19.1 - - + -
108B LEU* 4.0 24.2 - - + -
132B ILE* 5.3 1.8 - - + -
138B LEU* 4.4 16.2 - - + -
139B PRO* 3.4 32.3 - - + +
140B THR* 3.9 6.5 - - + -
141B ILE* 3.0 30.1 + - - +
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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