Contacts of the strand formed by residues 329 - 332 (chain F) in PDB entry 6GL7
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 PHE 329 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282F VAL* 5.0 8.5 - - + -
291F THR* 3.9 26.5 - - + -
293F VAL* 3.4 27.8 - - + -
324F TRP* 3.2 40.0 + + + +
325F ALA* 3.0 31.3 - - - +
328F THR* 1.3 98.1 + - - +
330F ARG* 1.3 61.0 + - - +
340F VAL* 3.8 23.6 - - + -
341F GLN* 3.2 16.4 - - - -
342F ALA* 3.4 21.5 - - + -
352F HIS* 5.4 4.0 - + - +
374F VAL* 5.2 7.0 - - + -
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Residues in contact with ARG 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F ASP* 5.6 0.4 + - - -
325F ALA 5.7 0.2 - - - +
328F THR 5.4 3.3 + - - +
329F PHE* 1.3 73.6 - - - +
331F VAL* 1.3 66.6 + - - +
332F GLU* 2.9 25.7 + - - +
339F SER 3.6 0.5 - - - +
340F VAL* 3.2 8.4 - - - +
341F GLN* 2.9 69.1 + - + +
342F ALA* 5.0 0.2 - - - +
343F ASN* 2.9 32.3 + - - +
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Residues in contact with VAL 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F SER* 4.6 18.7 + - - +
317F THR* 3.7 28.3 - - + -
330F ARG* 1.3 80.2 - - - +
332F GLU* 1.3 67.6 + - - +
333F HIS* 3.5 21.8 + - + +
334F TRP* 5.6 0.7 - - - -
338F THR* 4.7 6.3 - - + -
339F SER 3.5 5.2 - - - +
340F VAL* 4.1 9.0 - - + -
356F LEU* 3.6 38.1 - - + -
357F VAL 5.6 1.3 - - - +
358F LEU* 5.9 0.4 - - + -
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Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330F ARG* 2.9 32.3 + - - +
331F VAL* 1.3 72.4 - - - +
333F HIS* 1.3 60.3 + - - +
334F TRP* 2.6 39.0 + - - +
335F PRO* 3.5 19.9 - - + +
337F GLU* 5.0 1.6 - - - +
338F THR* 2.9 25.7 + - - -
339F SER* 2.7 25.3 + - - +
341F GLN* 3.1 28.7 - - + +
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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