Contacts of the strand formed by residues 309 - 313 (chain A) in PDB entry 3CQ6
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 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASN* 3.5 27.6 - - - +
170A PRO* 5.5 0.2 - - + -
171A ASN 3.1 25.1 - - - -
172A ASN* 3.8 9.4 - - + -
173A PRO* 3.3 31.4 - - + -
174A THR 5.0 0.2 - - - -
175A GLY* 3.7 6.5 - - - -
200A TYR* 3.7 23.3 - + - -
305A SER* 2.8 24.8 + - - -
307A SER* 3.0 29.5 + - - +
308A ASN* 1.3 90.6 - - - +
310A VAL* 1.3 70.0 + - - +
342A ARG* 3.8 10.3 - - + -
343A THR 3.1 17.0 - - - +
345A ILE* 3.9 4.2 - - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 3.7 25.6 - - + +
291A VAL* 4.8 1.1 - - + -
292A ALA* 4.1 18.2 - - + +
295A LEU* 4.2 18.4 - - + -
302A VAL* 3.4 32.3 - - + -
303A VAL 4.7 2.0 - - - +
305A SER* 4.6 6.3 - - - -
309A PHE* 1.3 81.3 - - - +
311A PHE* 1.3 64.9 + - - +
312A PHE* 3.7 2.8 - - - -
342A ARG* 3.5 5.4 - - - -
343A THR* 2.9 41.3 + - + +
345A ILE* 4.2 9.9 - - + -
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 5.3 0.4 - - + -
146A PHE* 4.0 21.8 - + - -
173A PRO* 3.2 38.4 + - + +
174A THR* 4.0 23.8 + - + +
302A VAL* 3.7 3.8 - - - +
303A VAL* 3.1 51.6 + - + +
310A VAL* 1.3 70.8 - - - +
312A PHE* 1.3 61.7 + - - +
335A VAL* 3.7 23.3 - - + -
337A ILE* 4.0 19.5 - - + -
340A HIS* 3.3 40.4 - + + -
341A LEU 3.5 13.5 - - - -
342A ARG* 4.3 2.5 - - + +
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.9 22.7 - - + -
300A TYR* 3.7 30.1 - + + -
301A ALA 3.2 11.9 - - - +
302A VAL* 4.3 7.9 - - + -
310A VAL* 3.7 9.9 - - + -
311A PHE* 1.3 75.8 - - - +
313A GLY* 1.3 59.0 + - - +
315A PHE* 3.9 21.9 - + - -
325A PHE* 4.1 10.3 - + - -
332A ILE* 3.9 15.9 - - + -
340A HIS* 3.1 10.0 - - - -
341A LEU* 3.0 57.9 + - + -
343A THR* 4.0 9.6 - - + -
354A PHE* 3.7 33.2 - + - -
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Residues in contact with GLY 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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300A TYR* 3.4 20.1 - - - -
301A ALA* 2.8 36.1 + - - -
312A PHE* 1.3 74.5 - - - +
314A ASP* 1.3 60.4 + - - -
315A PHE* 4.1 5.6 - - - -
339A GLY 3.1 10.5 - - - -
340A HIS* 3.9 9.1 - - - -
405A PO4 3.8 1.4 + - - -
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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