Contacts of the strand formed by residues 325 - 329 (chain D) in PDB entry 6B5G
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 ARG 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290D LYS* 2.7 57.5 + - - +
291D SER 3.4 4.8 + - - +
292D PRO* 3.3 14.2 - - + +
293D ASN 2.8 23.8 + - - -
323D GLY 3.3 0.4 - - - -
324D SER* 1.3 81.9 - - - +
326D ILE* 1.3 63.6 + - - +
327D PHE* 3.4 26.1 - - + -
409D ASP* 5.9 1.0 + - - -
414D ALA* 3.8 20.8 + - + +
426D LEU* 3.9 16.1 - - + +
437D ARG 2.7 29.5 + - - -
438D ALA* 3.1 21.8 + - - +
440D ASN 4.0 10.7 + - - -
441D SER* 4.1 13.8 + - - -
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Residues in contact with ILE 326 (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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293D ASN* 3.2 21.3 - - + +
295D ILE* 3.9 21.3 - - + -
308D ALA* 3.8 15.9 - - + +
312D VAL* 3.8 10.5 - - + -
323D GLY 3.4 15.3 - - - +
325D ARG* 1.3 69.6 - - - +
327D PHE* 1.3 56.3 + - - +
328D VAL* 4.0 5.2 - - + -
336D PHE* 4.0 17.0 - - + -
423D GLN* 3.2 44.0 - - + +
424D GLU 3.1 12.5 + - - +
425D ILE* 3.4 5.4 - - + +
426D LEU* 2.7 33.7 + - - +
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Residues in contact with PHE 327 (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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292D PRO* 3.8 23.8 - - + -
293D ASN 2.7 12.5 + - - +
294D ILE* 4.4 5.6 - - + -
295D ILE* 2.7 35.5 + - - +
325D ARG* 3.4 44.4 - - + -
326D ILE* 1.3 71.4 - - - +
328D VAL* 1.3 57.8 + - - +
409D ASP* 3.9 4.5 - - - -
426D LEU* 3.5 26.0 - - + -
427D ARG 4.8 2.2 - - - -
428D PHE* 3.7 5.3 - - + -
434D VAL* 3.6 29.8 - - + -
437D ARG* 3.5 45.5 - - + -
438D ALA* 4.3 7.0 - - + -
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Residues in contact with VAL 328 (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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295D ILE* 3.6 7.6 - - + +
326D ILE* 4.0 7.4 - - + -
327D PHE* 1.3 79.0 - - - +
329D GLU* 1.3 65.3 + - - +
332D ILE* 3.5 26.7 - - + -
333D TYR* 3.6 29.4 - - + -
336D PHE* 3.6 37.9 - - + -
425D ILE* 3.8 13.7 - - + -
426D LEU 2.9 10.2 + - - +
427D ARG* 3.4 6.8 - - - +
428D PHE* 3.1 22.9 + - - -
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Residues in contact with GLU 329 (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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295D ILE 3.0 12.3 + - - +
296D PHE* 3.6 18.6 - - - +
297D ALA* 2.6 52.9 + - + +
298D ASP 4.7 0.2 + - - -
328D VAL* 1.3 71.6 - - - +
330D GLU* 1.3 69.5 + - - +
331D SER* 3.1 6.5 - - - +
332D ILE* 2.9 16.8 + - + +
333D TYR 3.0 9.4 + - - -
428D PHE* 3.1 25.2 - - + +
429D LYS* 4.3 13.0 - - + +
456D LYS* 5.4 4.8 + - - -
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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