Contacts of the strand formed by residues 162 - 170 (chain B) in PDB entry 3SKU
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 GLY 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.7 16.2 - - - -
160B THR 3.2 7.5 + - - -
161B ALA* 1.3 73.9 - - - +
163B THR* 1.3 63.4 + - - -
164B TYR* 3.7 4.8 - - - -
180B ILE* 3.9 6.1 - - - +
181B LEU 3.3 28.2 + - - +
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Residues in contact with THR 163 (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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101B ARG* 3.8 2.9 - - - +
102B MET* 2.9 46.2 + - + +
162B GLY* 1.3 71.6 - - - -
164B TYR* 1.3 73.8 + - - +
165B LEU* 5.1 0.4 - - + -
178B GLN* 4.0 29.2 - - + +
179B PHE 3.7 6.3 - - - +
180B ILE* 4.2 19.6 - - + +
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Residues in contact with TYR 164 (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 LEU* 3.7 22.2 - - + -
99B TRP* 4.2 5.4 - + + -
100B PHE 3.6 4.5 - - - -
101B ARG* 3.6 18.7 + - - -
102B MET* 4.5 0.2 - - - -
110B ILE* 4.0 16.8 - - + -
138B TYR* 2.7 38.9 + + - -
151B PHE* 4.8 3.6 - + - -
153B MET* 3.6 24.7 - - + -
160B THR* 3.0 39.9 + - - +
162B GLY 3.7 13.5 - - - -
163B THR* 1.3 79.9 - - - +
165B LEU* 1.3 66.4 + - - +
166B ARG 4.4 0.2 - - - -
178B GLN* 3.4 3.8 - - - -
179B PHE* 2.7 45.1 + - - +
181B LEU* 4.6 8.1 - - + -
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Residues in contact with LEU 165 (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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47B PRO* 4.2 23.8 - - + +
55B ILE* 5.8 1.3 - - + -
98B ALA 3.5 0.7 - - - +
99B TRP* 3.4 9.5 - - - -
100B PHE* 3.1 36.6 + - + +
102B MET* 3.8 37.5 - - + -
163B THR* 5.1 0.4 - - + -
164B TYR* 1.3 83.7 - - - +
166B ARG* 1.3 60.7 + - - +
176B ILE* 3.3 24.2 - - + -
177B THR 3.3 21.3 - - - +
178B GLN* 3.9 23.3 - - + +
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Residues in contact with ARG 166 (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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72B ASN* 4.8 0.2 + - - -
73B ALA* 3.5 33.5 + - - +
74B PRO 4.4 1.4 + - - -
75B SER* 3.4 17.3 - - - +
97B ILE* 4.8 3.4 - - + -
98B ALA 3.3 4.9 - - - +
99B TRP* 3.5 34.9 - - + +
100B PHE* 5.3 0.7 - - - -
149B LEU* 3.2 41.2 + - - +
165B LEU* 1.3 75.6 - - - +
167B LEU* 1.3 74.7 + - - +
168B VAL* 4.0 15.2 - - + +
175B GLU* 2.7 29.7 + - - -
176B ILE* 3.6 22.9 - - - +
177B THR* 2.7 35.7 + - - -
179B PHE* 4.2 8.1 - - + -
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Residues in contact with LEU 167 (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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45B PRO* 3.5 38.8 - - + -
46B ASP 4.4 13.0 - - - +
47B PRO* 4.7 5.2 - - + -
96B THR 4.1 1.3 - - - +
97B ILE* 3.1 9.0 - - - +
98B ALA* 2.7 45.3 + - + +
100B PHE* 4.4 9.6 - - + -
166B ARG* 1.3 75.8 - - - +
168B VAL* 1.3 87.4 + - - +
169B LYS* 3.8 8.3 - - + -
174B THR* 3.4 32.3 - - + -
175B GLU 4.1 4.5 - - - +
176B ILE* 4.7 8.1 - - + -
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Residues in contact with VAL 168 (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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75B SER* 4.1 3.8 - - - +
77B ALA* 3.6 27.6 - - + -
95B LEU* 3.7 19.7 - - + -
96B THR 3.5 2.9 - - - -
97B ILE* 4.2 9.9 - - + -
124B LEU* 5.1 0.4 - - + -
149B LEU* 3.9 25.1 - - + -
166B ARG* 4.0 18.4 - - - +
167B LEU* 1.3 79.3 - - - +
169B LYS* 1.3 60.6 + - - +
170B ILE* 4.7 1.1 - - + -
173B TRP* 3.6 13.6 - - + -
174B THR* 3.6 0.2 - - - -
175B GLU* 3.1 39.0 + - + +
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Residues in contact with LYS 169 (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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41B GLN* 5.7 2.8 + - - -
45B PRO* 4.5 20.9 - - + +
49B GLN* 5.9 5.1 - - - +
94B ASN 3.3 5.0 - - - +
95B LEU 3.4 0.2 - - - -
96B THR* 2.8 49.9 + - + +
167B LEU* 3.8 14.8 - - + -
168B VAL* 1.3 74.1 - - - +
170B ILE* 1.3 63.0 + - - +
171B ASN* 3.0 26.7 + - - +
172B ASP* 5.0 1.8 - - - +
173B TRP 3.0 18.6 - - - +
174B THR* 3.8 13.2 - - + +
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Residues in contact with ILE 170 (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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77B ALA* 4.4 19.3 - - + +
80B ILE* 4.9 11.0 - - + -
81B VAL* 3.7 27.8 - - + -
93B TYR* 3.9 28.7 - - + -
94B ASN 3.4 2.9 - - - +
95B LEU* 3.5 23.8 - - + -
120B TYR* 5.7 1.6 - - + +
124B LEU* 3.9 17.7 - - + -
168B VAL* 4.2 1.5 - - + -
169B LYS* 1.3 70.0 - - - +
171B ASN* 1.3 61.1 + - + +
172B ASP 2.7 18.0 + - - -
173B TRP* 2.9 34.5 + - + +
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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