Contacts of the strand formed by residues 321 - 326 (chain A) in PDB entry 6H0F
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 VAL 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA 6.1 1.6 - - - +
316A TYR* 3.6 5.0 - - - -
317A LEU* 2.9 33.5 + - + +
318A ASP 3.0 17.9 + - - +
319A ASN* 3.9 7.6 - - + +
320A GLY* 1.4 79.7 - - - +
322A VAL* 1.3 62.8 + - - +
333A LEU* 3.7 28.7 - - + -
334A VAL 3.4 7.9 - - - +
335A LYS* 4.0 17.7 - - + +
350A MET* 3.8 25.1 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 3.5 34.5 - - + -
280A LEU* 5.3 4.0 - - + -
314A LEU* 4.3 16.2 - - + -
315A THR 3.6 12.8 - - - +
316A TYR* 3.9 9.9 - - + -
317A LEU* 4.7 0.2 - - - -
321A VAL* 1.3 82.6 - - - +
323A PHE* 1.4 71.1 + - - +
324A VAL* 3.8 5.5 + - + -
333A LEU* 3.5 2.8 - - - +
334A VAL* 2.9 43.7 + - + +
336A LEU* 3.7 25.1 - - + -
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Residues in contact with PHE 323 (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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15A VAL* 4.3 9.2 - - + -
18A CYS* 3.9 28.7 - - + -
31A LEU* 3.8 21.3 - - + -
33A ILE* 3.8 26.7 - - + -
49A LEU* 4.7 1.6 - - + -
314A LEU* 3.6 5.2 - - - -
315A THR* 2.9 43.7 + - + +
317A LEU* 4.2 11.0 - - + +
322A VAL* 1.4 71.8 - - - +
324A VAL* 1.3 59.0 + - - +
325A GLY* 3.7 26.0 - - - -
331A SER* 4.0 11.2 - - - -
332A GLN 3.1 23.8 - - - -
333A LEU* 4.2 5.4 - - + -
353A PHE* 3.6 28.5 - + - -
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Residues in contact with VAL 324 (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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308A THR* 3.8 16.8 - - + +
309A SER* 4.0 8.3 - - - +
311A ALA* 3.7 29.2 - - + -
314A LEU* 4.0 14.6 - - + -
322A VAL* 4.3 3.4 - - + +
323A PHE* 1.3 72.2 - - - +
325A GLY* 1.3 59.0 + - - +
331A SER* 3.2 9.2 - - - -
332A GLN* 2.9 53.1 + - - +
334A VAL* 4.0 37.7 - - + -
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Residues in contact with GLY 325 (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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15A VAL* 3.8 12.1 - - - -
311A ALA* 3.5 2.3 - - - -
312A GLU* 2.7 33.1 + - - -
313A CYS* 2.9 25.8 + - - +
323A PHE* 3.7 23.5 + - - -
324A VAL* 1.3 70.6 - - - +
326A SER* 1.4 52.2 + - - -
331A SER* 3.8 3.4 - - - -
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Residues in contact with SER 326 (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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15A VAL* 3.2 25.9 + - - +
309A SER* 4.0 9.4 - - - -
310A ILE 2.8 24.2 + - - -
311A ALA* 4.9 0.2 - - - -
312A GLU 4.2 0.4 - - - +
324A VAL 3.5 1.3 + - - -
325A GLY* 1.4 73.0 - - - -
327A ARG* 1.4 58.8 + - - +
329A GLY* 3.0 34.3 + - - -
330A ASP 3.6 15.5 - - - -
331A SER* 2.9 14.2 + - - -
355A ASN* 3.4 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