Contacts of the strand formed by residues 312 - 317 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LEU 3.4 12.6 - - - -
66D LEU* 4.4 2.7 - - - +
67D SER* 4.2 2.2 - - - +
166D GLU 5.0 0.7 - - - +
168D MET* 4.5 10.5 + - - +
310D PHE 3.0 8.9 + - - -
311D LEU* 1.3 75.2 - - - +
313D ASP* 1.3 59.4 + - - +
427D GLY* 6.2 2.2 - - - -
428D HIS 4.6 6.8 + - - +
429D PRO* 4.0 19.2 - - - +
430D PHE 4.7 2.3 + - - -
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Residues in contact with ASP 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D PRO 4.3 1.0 - - - +
64D PHE* 3.7 5.9 - - - +
65D LEU* 3.1 29.5 + - - +
67D SER* 5.1 1.6 - - - +
166D GLU 3.6 10.5 - - - -
167D LEU* 4.5 8.5 - - - +
168D MET 4.8 0.7 - - - +
312D THR* 1.3 75.0 - - - +
314D GLY* 1.3 58.1 + - - +
429D PRO* 5.6 2.5 - - - -
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Residues in contact with GLY 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D THR 5.0 2.2 - - - -
63D PRO 4.8 8.1 - - - -
64D PHE* 5.1 2.7 - - - -
164D GLY 4.1 0.7 - - - +
165D VAL* 3.8 0.7 - - - -
166D GLU 3.0 32.8 + - - +
313D ASP* 1.3 74.0 - - - +
315D ALA* 1.3 58.5 + - - -
429D PRO* 5.8 1.8 - - - +
432D ALA* 5.7 2.9 - - - -
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 4.1 1.7 - - - -
62D THR* 3.5 29.6 + - - +
79D LEU 5.1 12.3 - - - -
80D ALA* 5.8 1.3 - - - +
83D ALA* 6.0 2.9 - - - -
164D GLY 3.1 12.6 - - - -
165D VAL* 4.1 5.6 - - - +
314D GLY* 1.3 75.4 - - - -
316D SER* 1.3 57.8 + - - +
432D ALA* 5.8 2.2 - - - +
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Residues in contact with SER 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL 3.7 9.9 - - - -
61D ARG* 4.4 3.6 - - - +
62D THR 4.9 0.2 - - - +
83D ALA* 5.8 7.5 - - - +
163D GLY* 2.9 5.3 - - - -
164D GLY 2.9 30.6 + - - +
315D ALA* 1.3 75.4 - - - +
317D ALA* 1.3 57.0 + - - +
432D ALA 5.6 3.6 + - - -
435D CYS* 4.8 13.0 - - - -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLY* 3.4 4.0 - - - -
60D VAL* 2.8 31.1 + - - +
83D ALA 5.6 7.2 + - - -
84D LEU* 6.4 0.7 - - - +
162D ALA 3.3 13.0 - - - -
163D GLY* 3.9 2.0 - - - -
316D SER* 1.3 75.2 - - - +
318D MET* 1.3 58.8 + - - +
435D CYS* 4.6 9.0 + - - +
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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