Contacts of the strand formed by residues 307 - 312 (chain A) in PDB entry 4CQ8
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 ILE 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 4.0 13.7 - - + -
216A ASP 3.7 35.9 - - - +
217A PHE* 3.7 27.6 - - + -
238A LEU* 4.4 1.9 - - - +
243A SER 3.1 6.8 + - - +
244A PHE* 3.1 37.8 - - + -
245A ILE* 3.2 5.9 + - - +
305A LYS 4.0 5.8 - - - +
306A HIS* 1.3 76.9 - - - +
308A VAL* 1.3 67.6 + - - +
337A ASP* 3.5 23.3 - - + +
338A TYR* 4.2 20.9 - - + -
419A THR* 4.4 10.3 - - + -
420A THR* 5.5 2.0 - - + -
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Residues in contact with VAL 308 (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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234A ILE* 3.9 15.7 - - + -
238A LEU* 4.7 2.7 - - + -
245A ILE* 3.4 10.1 - - + +
247A ILE* 4.4 18.4 - - + -
290A LEU* 3.8 22.7 - - + -
293A PHE* 3.6 33.0 - - + -
294A ARG* 3.6 14.5 + - - +
306A HIS 5.1 0.9 - - - +
307A ILE* 1.3 78.8 - - - +
309A GLY* 1.3 70.3 - - - +
336A ALA* 3.9 2.1 - - - -
337A ASP* 2.9 37.3 + - - +
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Residues in contact with GLY 309 (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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245A ILE 2.9 9.9 + - - +
246A GLU* 4.0 3.6 - - - -
247A ILE* 2.9 27.4 + - - +
307A ILE 4.2 0.2 - - - -
308A VAL* 1.3 75.8 - - - +
310A VAL* 1.3 66.3 + - - +
338A TYR* 3.4 38.8 - - - -
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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
----------------------------------------------------------
246A GLU* 4.6 0.4 - - - -
247A ILE* 3.7 15.3 - - + +
250A ILE* 3.8 30.3 - - + -
290A LEU* 3.7 30.3 - - + -
308A VAL* 5.0 0.9 - - + -
309A GLY* 1.3 78.0 - - - +
311A SER* 1.3 66.8 + - - +
312A ILE* 3.8 5.1 + - + +
332A ILE* 3.9 16.6 - - + -
336A ALA* 3.8 13.2 - - + -
338A TYR* 3.0 8.3 + - - -
339A ILE* 3.4 18.6 - - + +
340A ALA* 2.9 24.3 + - - +
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA* 3.9 6.1 - - - -
246A GLU* 3.9 20.5 + - - +
247A ILE 2.9 17.8 + - - -
248A GLY* 3.9 0.7 - - - -
249A THR* 2.7 29.9 + - - -
250A ILE* 3.0 30.3 + - - +
309A GLY 4.2 0.2 - - - -
310A VAL* 1.3 71.9 - - - +
312A ILE* 1.3 60.3 + - - +
340A ALA* 3.4 11.0 + - - +
342A ASN* 3.7 12.6 + - - +
429A LYS* 5.9 0.7 - - - +
800A FMN 4.1 3.5 + - - -
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Residues in contact with ILE 312 (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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249A THR* 3.5 4.5 - - - -
250A ILE* 3.7 13.5 - - + +
310A VAL* 4.0 14.6 - - + +
311A SER* 1.3 79.4 + - - +
313A GLY* 1.3 57.9 + - - +
325A LEU* 3.8 46.6 - - + +
328A CYS* 3.6 25.1 - - + -
329A ILE* 4.0 12.1 - - + -
332A ILE* 4.8 4.0 - - + -
339A ILE* 3.6 26.5 - - + -
340A ALA 2.9 17.0 + - - +
341A ILE* 4.6 2.9 - - + -
342A ASN* 3.1 26.0 + - - +
367A VAL* 4.7 4.5 - - + -
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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