Contacts of the strand formed by residues 129 - 138 (chain B) in PDB entry 4PSQ
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 CYS 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B CYS 4.4 1.8 + - - -
6B VAL* 3.7 5.9 - - + +
118B TYR* 3.3 16.2 - - - +
120B CYS* 2.0 52.9 - - - -
122B LEU 3.5 0.4 - - - -
124B ASN* 3.2 8.8 + - - -
128B THR* 1.3 76.1 + - - +
130B ALA* 1.3 60.6 + - - +
131B ASP 3.3 25.6 - - - -
132B SER* 3.6 11.0 - - - +
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Residues in contact with ALA 130 (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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33B GLU* 4.3 9.4 - - - +
122B LEU* 2.7 35.4 + - + +
123B LEU 4.2 1.3 - - - +
124B ASN* 3.5 30.2 - - - +
128B THR 3.8 0.6 + - - -
129B CYS* 1.3 72.1 - - - +
131B ASP* 1.3 58.8 + - - +
132B SER 4.3 0.2 - - - -
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Residues in contact with ASP 131 (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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30B LYS* 5.2 1.0 + - - +
32B PRO* 3.5 9.0 - - - +
33B GLU* 2.9 49.9 + - - +
121B ARG* 2.8 54.0 + - + +
122B LEU* 3.4 21.8 + - + +
129B CYS* 3.3 3.2 - - - -
130B ALA* 1.3 81.2 - - - +
132B SER* 1.3 57.1 + - - +
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Residues in contact with SER 132 (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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30B LYS* 2.7 47.6 + - - +
31B ASP 3.1 7.8 - - - +
32B PRO* 3.3 8.9 - - - +
118B TYR* 3.9 17.9 - - - -
119B SER 3.2 12.1 - - - -
129B CYS* 3.6 17.9 - - - +
131B ASP* 1.3 76.5 + - - +
133B TYR* 1.3 60.4 + - - +
161B LEU* 3.8 11.7 - - - +
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Residues in contact with TYR 133 (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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30B LYS* 3.2 16.2 - - - +
32B PRO* 3.5 20.4 - - + -
36B PHE* 3.5 21.3 - + + -
88B MET* 3.6 21.0 - - - +
102B ASP* 2.9 32.5 + - - +
103B ASP 4.5 0.3 + - - -
117B GLN* 3.5 23.6 + - - -
118B TYR* 3.5 2.5 - - - -
119B SER* 2.9 53.7 + - - +
121B ARG* 3.6 26.7 - - - -
132B SER* 1.3 76.5 - - - +
134B SER* 1.3 66.0 + - - +
135B PHE* 4.1 13.9 - + - -
201B 2WL 3.7 11.4 - - + -
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Residues in contact with SER 134 (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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29B LYS* 3.2 8.1 - - - +
30B LYS* 3.0 28.0 + - - -
116B VAL* 4.2 3.8 - - - +
117B GLN* 2.6 25.3 + - - -
118B TYR* 4.4 4.0 - - - -
133B TYR* 1.3 79.2 - - - +
135B PHE* 1.3 63.2 + - - +
159B LEU* 4.4 0.9 - - - +
161B LEU* 4.0 13.2 - - - -
165B TYR* 2.6 37.1 + - - -
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Residues in contact with PHE 135 (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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26B ALA* 4.0 14.8 - - + -
28B ALA 3.7 1.1 - - - -
29B LYS* 3.9 21.5 - - + -
36B PHE* 3.8 24.2 - + - -
37B LEU* 5.3 0.4 - - + -
41B ILE* 3.9 35.4 - - + -
115B ALA 3.9 0.5 - - - +
116B VAL* 3.6 3.3 - - - +
117B GLN* 2.9 50.2 + - - +
133B TYR* 4.1 9.2 - + - -
134B SER* 1.3 76.8 + - - +
136B VAL* 1.3 63.4 + - - +
137B PHE* 3.5 37.2 - + + -
201B 2WL 3.8 40.4 - - + -
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Residues in contact with VAL 136 (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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26B ALA* 3.5 2.8 - - - -
27B MET* 2.9 31.6 + - + +
28B ALA* 2.9 24.5 + - + +
115B ALA 3.6 4.0 - - - +
116B VAL* 5.0 5.6 - - + -
135B PHE* 1.3 74.4 - - - +
137B PHE* 1.3 69.3 + - - +
144B LEU* 4.3 11.7 - - + -
152B VAL* 3.9 31.0 - - + -
156B GLN* 3.6 28.3 - - + +
165B TYR* 3.9 15.3 - - + -
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Residues in contact with PHE 137 (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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20B PHE* 5.0 7.2 - + - -
24B TRP* 3.5 37.2 - + + -
25B TYR 3.4 1.8 - - - -
26B ALA* 3.8 31.4 - - + -
41B ILE* 5.2 3.8 - - + -
43B ALA* 4.1 24.7 - - + -
45B PHE* 5.0 13.0 - + - -
104B HIS* 5.6 0.7 - + - -
114B TYR* 3.4 6.9 - - - +
115B ALA* 2.8 41.5 + - + +
117B GLN* 3.8 21.8 - - + -
135B PHE* 3.5 34.5 - + + -
136B VAL* 1.3 76.7 - - - +
138B SER* 1.3 62.3 + - - +
144B LEU* 3.9 3.1 - - - +
201B 2WL 5.0 6.5 - - + -
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Residues in contact with SER 138 (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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24B TRP* 3.7 5.8 - - - -
25B TYR* 2.7 39.7 + - - +
27B MET* 3.6 18.2 - - - -
113B THR 3.2 7.7 + - - -
137B PHE* 1.3 77.4 - - - +
139B ARG* 1.3 62.8 + - - +
140B ASP 2.6 29.8 + - - -
143B GLY 3.4 10.9 + - - -
144B LEU* 3.4 16.0 - - - +
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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