Contacts of the strand formed by residues 312 - 317 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H LEU 3.4 12.8 - - - -
66H LEU* 4.4 2.5 - - - +
67H SER* 4.2 2.0 - - - +
166H GLU 5.0 0.9 - - - +
168H MET* 4.5 10.9 + - - +
310H PHE 3.0 8.7 + - - -
311H LEU* 1.3 74.8 - - - +
313H ASP* 1.3 58.4 + - - +
427H GLY* 6.2 2.0 - - - -
428H HIS 4.6 7.6 + - - +
429H PRO* 4.0 19.4 - - - +
430H PHE 4.7 2.3 + - - -
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Residues in contact with ASP 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H PRO 4.3 1.0 - - - +
64H PHE* 3.7 6.0 - - - +
65H LEU* 3.1 31.0 + - - +
67H SER* 5.1 1.8 - - - +
166H GLU 3.6 10.3 - - - -
167H LEU* 4.5 8.7 - - - +
168H MET 4.8 1.1 - - - +
312H THR* 1.3 73.7 - - - +
314H GLY* 1.3 58.5 + - - +
429H PRO* 5.6 2.5 - - - -
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Residues in contact with GLY 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62H THR 5.0 2.2 - - - -
63H PRO 4.8 8.3 - - - -
64H PHE* 5.1 2.2 - - - -
164H GLY 4.1 0.7 - - - +
165H VAL* 3.8 0.9 - - - -
166H GLU 3.0 32.1 + - - +
313H ASP* 1.3 75.0 - - - +
315H ALA* 1.3 57.0 + - - -
429H PRO* 5.8 1.8 - - - +
432H ALA* 5.7 2.9 - - - -
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Residues in contact with ALA 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ARG* 4.1 1.7 - - - -
62H THR* 3.5 29.2 + - - +
79H LEU 5.1 13.2 - - - -
80H ALA* 6.1 1.1 - - - +
83H ALA* 6.0 2.9 - - - -
164H GLY 3.1 12.6 - - - -
165H VAL* 4.1 5.4 - - - +
314H GLY* 1.3 74.8 - - - -
316H SER* 1.3 57.5 + - - +
432H ALA* 5.8 2.2 - - - +
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Residues in contact with SER 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H VAL 3.7 9.4 - - - -
61H ARG* 4.4 3.4 - - - +
62H THR 4.9 0.2 - - - +
83H ALA* 5.8 7.5 - - - +
163H GLY* 2.9 5.1 - - - -
164H GLY 2.9 30.8 + - - +
315H ALA* 1.3 75.3 - - - +
317H ALA* 1.3 58.4 + - - +
432H ALA 5.6 3.4 - - - -
435H CYS* 4.8 12.6 - - - -
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Residues in contact with ALA 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H GLY* 3.4 3.8 - - - -
60H VAL* 2.8 31.1 + - - +
83H ALA 5.6 7.4 + - - -
84H LEU* 6.4 0.7 - - - +
162H ALA 3.3 13.2 - - - -
163H GLY* 3.9 2.2 - - - -
316H SER* 1.3 74.5 - - - +
318H MET* 1.3 59.0 + - - +
435H 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