Contacts of the strand formed by residues 312 - 316 (chain A) in PDB entry 1PHP
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 LEU 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 6.2 1.3 - - - -
181A ALA* 4.1 17.3 - - + -
185A PRO* 3.7 33.4 - - + -
186A ASP* 3.5 22.7 - - + +
188A PRO 3.4 4.1 + - - +
189A PHE* 3.6 22.9 - - + -
190A THR 3.0 24.4 + - - -
310A SER* 3.8 0.9 - - - -
311A LYS* 1.3 78.9 - - - +
313A VAL* 1.3 74.5 + - - +
314A VAL* 4.8 1.3 - - + -
345A TYR* 3.4 32.3 - - + +
347A VAL* 4.0 16.2 - - + -
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR* 3.2 15.0 - - - +
192A ILE* 3.9 22.0 - - + -
307A ILE* 4.5 10.8 - - + +
310A SER* 3.9 13.5 - - - -
312A LEU* 1.3 81.3 - - - +
314A VAL* 1.3 74.1 + - - +
315A TRP* 4.4 4.0 - - + +
338A LEU* 3.8 27.1 - - + -
344A THR* 3.6 18.8 - - + -
345A TYR 2.9 10.8 + - - +
346A SER* 3.6 0.2 - - - -
347A VAL* 2.8 28.9 + - - +
348A ILE* 6.4 0.2 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 4.2 16.2 - - + -
189A PHE* 3.6 30.1 - - + -
190A THR 3.0 6.2 + - - +
191A ALA* 3.2 6.0 - - + +
192A ILE 2.9 25.3 + - - +
193A ILE* 5.3 2.4 - - + +
208A LEU* 4.9 12.3 - - + -
312A LEU* 4.4 1.8 - - + -
313A VAL* 1.3 77.9 - - - +
315A TRP* 1.3 63.1 + - - +
316A ASN* 4.4 1.3 + - + +
347A VAL* 3.5 23.1 - - + +
380A MET* 4.0 33.2 - - + -
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Residues in contact with TRP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ILE* 3.4 29.8 - - + +
313A VAL* 4.1 3.1 - - + -
314A VAL* 1.3 76.7 - - - +
316A ASN* 1.3 71.1 + - - +
317A GLY 2.8 31.7 + - - -
318A PRO* 4.6 2.9 - - + -
319A MET* 4.1 8.0 - - + +
331A THR* 3.9 40.4 - - + -
334A ILE* 4.1 22.9 - - + -
335A ALA* 4.1 14.6 - - + -
338A LEU* 3.7 24.5 - - + -
347A VAL 2.9 11.5 + - - +
348A ILE* 3.5 25.0 - - + +
349A GLY 3.1 24.4 + - - +
353A SER* 4.9 8.1 - - - -
356A ALA* 5.5 0.4 - - + -
357A VAL* 3.9 25.6 - - + -
366A MET* 5.8 0.2 - - + -
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ILE 3.0 7.5 + - - -
193A ILE* 3.2 20.8 - - + +
194A GLY 2.8 27.2 + - - +
201A LYS* 2.8 30.8 + - - +
204A VAL* 5.4 3.8 - - + +
314A VAL* 4.3 0.8 - - + +
315A TRP* 1.3 73.5 - - - +
317A GLY* 1.3 55.6 + - - +
349A GLY* 3.0 23.1 + - - +
350A GLY* 3.6 4.4 - - - -
353A SER* 4.1 0.4 - - - -
377A LEU* 3.8 20.1 - - + +
380A MET* 5.1 8.3 - - + -
396A ADP 2.8 26.9 + - - -
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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