Contacts of the strand formed by residues 52 - 59 (chain B) in PDB entry 5VSW
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 PRO 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU 6.4 0.4 - - - +
8A PHE* 5.6 2.7 - - + -
50B SER 3.2 8.7 - - - +
51B MET* 1.3 97.4 - - + +
53B GLY* 1.3 60.1 + - - +
148B ARG* 5.6 10.1 - - - +
149B GLY 3.7 5.8 - - - +
150B ARG* 3.9 20.4 - - + +
177B TYR 3.8 3.6 - - - +
179B PRO* 4.0 9.2 - - - +
219B ARG* 5.7 12.8 - - + +
223B ILE* 4.7 9.0 - - + -
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Residues in contact with GLY 53 (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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52B PRO* 1.3 77.0 - - - +
54B CYS* 1.3 64.8 + - - -
148B ARG* 3.3 8.3 - - - +
149B GLY 2.7 38.5 + - - +
177B TYR* 2.9 26.1 - - - +
179B PRO* 5.3 1.1 - - - -
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Residues in contact with CYS 54 (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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53B GLY* 1.3 73.7 - - - -
55B ALA* 1.3 64.5 + - - +
89B ALA* 5.5 0.5 - - - -
90B VAL* 3.0 29.8 + - + +
91B ARG* 3.8 7.4 - - - -
92B VAL* 3.2 39.3 - - + +
146B VAL* 4.4 8.5 - - + -
147B GLN 3.6 15.5 - - - +
148B ARG* 3.6 27.8 - - + -
176B CYS 4.8 0.2 - - - +
177B TYR* 4.0 3.5 + - - +
208B ASN* 5.9 1.0 + - - -
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Residues in contact with ALA 55 (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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54B CYS* 1.3 77.1 - - - +
56B VAL* 1.3 69.6 + - - +
57B THR* 3.1 4.2 + - - -
86B LYS 4.9 2.0 - - - +
88B LEU 4.7 10.5 - - - +
90B VAL* 5.4 1.8 - - - +
146B VAL* 3.6 11.9 - - - +
147B GLN 3.6 2.3 + - - +
176B CYS* 3.2 46.2 - - - +
177B TYR* 3.1 23.9 - - + -
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Residues in contact with VAL 56 (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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55B ALA* 1.3 73.0 - - - +
57B THR* 1.3 60.7 + - - +
59B VAL* 4.0 11.2 - - + -
85B LEU* 3.7 32.4 + - + +
86B LYS* 5.5 1.3 + - - +
88B LEU* 4.3 16.8 - - + +
90B VAL* 4.9 2.7 - - + -
144B ILE* 3.6 42.4 - - + -
145B LYS 4.0 4.0 - - - +
146B VAL* 4.0 13.9 - - + +
173B VAL* 3.0 30.9 - - + +
174B ASP 3.9 9.9 - - - +
175B ALA* 3.9 5.0 - - - -
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Residues in contact with THR 57 (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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55B ALA 3.1 2.8 + - - -
56B VAL* 1.3 72.7 - - - +
58B GLU* 1.3 68.9 + - + +
145B LYS 3.2 7.1 + - - -
146B VAL* 4.2 0.2 - - - +
147B GLN* 3.2 43.6 + - - +
158B ARG* 6.3 3.4 - - - +
172B LEU* 4.0 6.3 - - + +
173B VAL* 3.0 26.9 + - - +
175B ALA* 4.6 4.4 - - + +
177B TYR* 2.6 41.3 + - - +
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Residues in contact with GLU 58 (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 VAL* 4.0 0.9 - - - +
57B THR* 1.3 91.1 - - + +
59B VAL* 1.3 72.9 + - - +
145B LYS* 3.0 57.7 + - + +
147B GLN* 3.2 18.3 - - - +
158B ARG* 4.8 13.3 + - - -
172B LEU* 4.1 25.1 - - + +
173B VAL 4.8 0.2 - - - -
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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 VAL* 4.0 8.7 - - + -
58B GLU* 1.3 87.8 - - - +
60B GLU* 1.3 62.7 + - - +
61B ILE* 3.6 29.8 + - + +
82B LEU* 5.1 7.0 - - + -
85B LEU* 3.6 30.3 - - + -
142B MET* 4.4 10.1 - - - -
143B ARG 4.7 4.3 - - - -
144B ILE* 4.2 10.5 - - + -
145B LYS* 5.9 0.2 - - - -
172B LEU* 4.0 19.2 + - - +
173B VAL* 4.4 12.3 - - + -
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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