Contacts of the strand formed by residues 312 - 317 (chain B) in PDB entry 5ZRV
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 THR 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU 3.4 12.1 - - - -
66B LEU* 4.4 3.1 - - - +
67B SER* 4.2 2.2 - - - +
166B GLU 5.0 0.7 - - - +
168B MET* 4.5 10.3 + - - +
310B PHE 3.0 9.9 + - - -
311B LEU* 1.3 74.6 - - - +
313B ASP* 1.3 58.7 + - - +
427B GLY* 6.2 2.0 - - - -
428B HIS 4.6 7.0 + - - +
429B PRO* 4.0 19.4 - - - +
430B PHE 4.7 2.3 + - - -
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Residues in contact with ASP 313 (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 PRO 4.3 1.0 - - - +
64B PHE* 3.7 5.8 - - - -
65B LEU* 3.1 30.2 + - - +
67B SER* 5.1 1.4 - - - +
166B GLU 3.6 10.3 - - - -
167B LEU* 4.5 8.7 - - - +
168B MET 4.8 0.7 - - - +
312B THR* 1.3 75.1 - - - +
314B GLY* 1.3 56.8 + - - +
429B PRO* 5.6 2.7 - - - -
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Residues in contact with GLY 314 (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 THR 5.0 1.8 - - - -
63B PRO 4.8 8.7 - - - -
64B PHE* 5.1 2.5 - - - -
164B GLY 4.1 0.9 - - - +
165B VAL* 3.8 0.7 - - - -
166B GLU 3.0 33.1 + - - +
313B ASP* 1.3 74.8 - - - +
315B ALA* 1.3 59.2 + - - -
429B PRO* 5.8 1.8 - - - +
432B ALA* 5.7 2.9 - - - -
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Residues in contact with ALA 315 (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 ARG* 4.1 1.7 - - - -
62B THR* 3.5 29.2 + - - +
79B LEU 5.1 12.6 - - - -
80B ALA* 6.1 0.9 - - - +
83B ALA* 6.0 2.9 - - - -
164B GLY 3.1 11.9 - - - -
165B VAL* 4.1 5.6 - - - +
314B GLY* 1.3 74.3 - - - -
316B SER* 1.3 58.4 + - - +
432B ALA* 5.8 2.5 - - - +
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Residues in contact with SER 316 (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 VAL 3.7 8.7 - - - -
61B ARG* 4.4 3.8 - - - +
62B THR 4.9 0.4 - - - +
83B ALA* 5.8 7.0 - - - +
163B GLY* 2.9 4.9 - - - -
164B GLY 2.9 31.0 + - - +
315B ALA* 1.3 74.3 - - - +
317B ALA* 1.3 58.3 + - - +
432B ALA 5.6 2.9 - - - -
435B CYS* 4.8 12.8 - - - -
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Residues in contact with ALA 317 (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 GLY* 3.4 4.3 - - - -
60B VAL* 2.8 31.5 + - - +
83B ALA 5.6 7.2 + - - -
84B LEU* 6.4 0.7 - - - +
162B ALA 3.3 12.3 - - - -
163B GLY* 3.9 2.5 - - - -
316B SER* 1.3 74.5 - - - +
318B MET* 1.3 57.4 + - - +
435B CYS* 4.6 8.0 + - - +
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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