Contacts of the strand formed by residues 309 - 314 (chain A) in PDB entry 2W7P
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 ALA 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ILE* 4.0 13.2 - - + -
107A ASP 3.3 17.9 - - - +
108A MET* 3.3 28.5 - - - -
109A ASP* 3.2 7.8 + - - -
298A ARG* 3.4 31.4 + - + +
301A ILE* 5.5 4.4 - - + +
308A THR* 1.3 77.2 - - - +
310A SER* 1.3 62.7 + - - +
330A ASN* 4.3 3.9 - - - +
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Residues in contact with SER 310 (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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106A ILE* 3.8 2.3 - - - +
107A ASP* 3.0 29.8 + - - +
109A ASP* 3.2 3.0 + - - -
309A ALA* 1.3 76.0 - - - +
311A ALA* 1.3 65.1 + - - +
324A SER* 3.2 15.3 - - - -
328A LYS* 2.8 53.9 - - - +
330A ASN 3.3 6.4 + - - -
331A GLY 3.0 14.8 - - - +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.5 6.1 - - + -
105A HIS 3.1 16.4 - - - +
106A ILE* 4.4 7.2 - - + -
294A VAL* 3.9 26.7 - - + -
298A ARG* 4.4 8.1 - - + -
310A SER* 1.3 78.6 - - - +
312A GLY* 1.3 59.2 + - - +
313A ILE* 5.1 0.2 - - - -
324A SER* 3.4 11.1 + - - -
331A GLY 2.9 6.1 + - - -
332A GLN* 2.9 30.6 - - + +
333A TYR 3.2 2.3 + - - -
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Residues in contact with GLY 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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103A ILE 3.9 0.3 - - - +
104A VAL* 3.3 6.8 - - - +
105A HIS* 3.0 31.7 + - - +
311A ALA* 1.3 73.0 - - - +
313A ILE* 1.3 65.4 + - - +
314A ALA 4.2 0.4 - - - -
320A ALA* 3.9 7.0 - - - +
323A CYS* 3.6 6.1 - - - -
324A SER* 3.3 23.1 - - - +
333A TYR 3.4 7.2 - - - -
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Residues in contact with ILE 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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102A THR* 3.9 18.8 - - + -
103A ILE 3.4 12.8 - - - +
104A VAL* 4.1 7.9 - - + -
290A ALA* 4.0 11.4 - - + +
291A GLN* 3.7 26.9 - - - +
294A VAL* 4.0 32.3 - - + -
311A ALA 5.0 1.3 - - - +
312A GLY* 1.3 79.7 - - - +
314A ALA* 1.3 60.0 + - - +
323A CYS* 4.1 2.7 - - - +
332A GLN* 4.5 6.1 - - - +
333A TYR 2.9 13.4 + - - +
334A GLN* 3.1 27.2 - - + +
335A ILE* 2.8 29.0 + - - +
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Residues in contact with ALA 314 (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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101A ASN 4.4 0.2 - - - -
102A THR* 5.0 2.2 - - - -
103A ILE* 2.9 32.2 + - - +
312A GLY 4.2 0.6 - - - -
313A ILE* 1.3 75.4 - - - +
315A PRO* 1.3 71.4 - - + +
316A ASN 3.1 6.0 + - - +
319A LEU* 3.3 37.7 - - + +
320A ALA* 3.7 13.2 - - - +
323A CYS* 4.8 0.4 - - - -
335A ILE* 4.0 9.4 - - + -
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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