Contacts of the strand formed by residues 11 - 15 (chain A) in PDB entry 2XFR
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 GLN 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.9 4.3 + - + -
10A VAL* 1.3 78.9 - - - +
12A VAL* 1.3 60.1 + - - +
13A TYR* 2.7 41.8 + - + -
46A ASP* 3.3 16.1 - - - +
83A LYS* 2.9 22.4 + - - +
412A PHE* 4.4 18.8 + - - +
413A GLY* 3.5 1.3 - - - -
414A PHE 2.9 26.2 + - - -
449A VAL* 3.6 21.9 + - + +
450A ASP* 2.9 38.4 + - - +
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Residues in contact with VAL 12 (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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10A VAL 3.9 1.3 - - - +
11A GLN* 1.3 77.0 - - - +
13A TYR* 1.3 74.8 + - - +
45A VAL* 3.5 7.0 - - + +
46A ASP* 2.9 39.8 + - - +
414A PHE* 3.4 8.7 - - + +
416A TYR* 5.2 0.9 - - + -
432A PHE* 4.5 11.2 - - + -
435A PHE* 4.4 15.7 - - + -
436A VAL* 4.2 31.0 - - + -
439A MET* 3.6 41.5 - - + -
440A HIS* 4.6 0.9 - - - +
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Residues in contact with TYR 13 (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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11A GLN* 2.7 46.4 + - + -
12A VAL* 1.3 80.9 - - - +
14A VAL* 1.3 66.8 + - - +
46A ASP* 4.3 4.9 - - + -
47A GLY* 3.1 33.7 - - - -
48A VAL* 3.6 9.0 - - - +
49A MET* 4.9 0.4 - - + +
83A LYS* 3.7 19.0 + - + -
85A GLN* 3.7 43.9 + - + +
173A VAL* 3.6 17.1 - - + +
413A GLY* 5.4 3.8 - - - -
414A PHE 2.8 14.3 + - - +
415A THR* 3.3 22.9 - - + +
416A TYR 2.8 23.5 + - - -
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Residues in contact with VAL 14 (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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12A VAL* 4.8 0.9 - - + -
13A TYR* 1.3 78.6 - - - +
15A MET* 1.3 75.0 + - - +
16A LEU* 3.5 0.3 + - - +
40A LEU* 3.8 22.4 - - + -
45A VAL* 4.0 15.0 - - + -
47A GLY 3.0 6.8 + - - +
48A VAL* 3.1 11.3 - - + +
49A MET 3.0 20.0 + - - -
415A THR* 4.3 1.1 - - - -
416A TYR* 3.7 13.9 - - + +
418A ARG 4.4 0.9 - - - -
419A LEU* 3.7 26.2 - - + +
423A LEU* 4.5 4.7 - - + -
432A PHE* 3.7 31.6 - - + -
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Residues in contact with MET 15 (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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14A VAL* 1.3 69.9 - - - +
16A LEU* 1.3 61.6 + - - +
49A MET* 3.5 42.8 - - + +
50A VAL* 4.2 3.6 - - - -
51A ASP* 4.7 4.5 - - - +
87A ILE* 4.2 18.2 - - + -
176A GLU* 5.9 0.2 - - - +
293A LYS* 6.1 1.1 - - - -
378A GLU* 3.6 24.9 - - - +
415A THR* 3.8 3.7 - - + +
416A TYR 2.9 17.8 + - - +
417A LEU* 3.9 23.3 - - + -
418A ARG* 3.4 37.4 - - + +
419A LEU* 2.8 32.2 + - - +
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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