Contacts of the strand formed by residues 8 - 14 (chain A) in PDB entry 2F24
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.4 6.4 - - - +
7A LEU* 1.3 81.3 - - - +
9A LYS* 1.3 67.7 + - - +
10A GLU* 3.0 26.5 + - + +
65A GLN* 3.6 20.8 + - - +
66A VAL* 2.7 48.2 + - - +
68A TRP* 3.9 9.9 - - - +
364A PHE* 3.8 14.0 - - + -
365A LEU* 3.2 8.3 - - - +
366A MET* 2.9 42.7 + - + +
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Residues in contact with LYS 9 (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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6A VAL* 4.4 9.9 - - + -
8A GLN* 1.3 77.5 - - - +
10A GLU* 1.3 63.8 + - - +
327A LEU 4.7 4.0 + - - +
328A ALA* 4.4 13.9 - - - +
329A LYS 5.7 0.6 - - - +
354A TYR* 3.7 22.6 + - - -
363A VAL* 4.0 11.2 - - + -
364A PHE 3.3 3.6 - - - -
365A LEU* 3.5 20.0 - - + -
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Residues in contact with GLU 10 (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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8A GLN* 3.0 29.5 + - + +
9A LYS* 1.3 77.7 - - - +
11A SER* 1.3 75.0 + - - +
12A VAL* 3.2 7.3 + - + +
55A ARG* 4.9 5.4 + - - -
66A VAL 4.4 1.2 - - - +
68A TRP* 3.7 26.5 + - + +
363A VAL* 4.1 3.4 - - - -
364A PHE* 2.8 39.8 + - + +
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Residues in contact with SER 11 (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 GLU* 1.3 80.6 - - - +
12A VAL* 1.3 59.8 + - - +
13A PHE 3.5 0.7 - - - -
14A GLN* 3.8 31.5 + - - +
55A ARG* 4.5 3.1 + - - -
361A GLU* 2.8 27.8 + - - -
362A ILE 3.7 8.7 - - - -
363A VAL* 4.0 10.2 - - - +
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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 GLU* 3.8 11.7 - - - +
11A SER* 1.3 76.2 - - - +
13A PHE* 1.3 76.4 + - + +
14A GLN* 5.5 0.2 - - - -
36A ALA* 5.1 1.8 - - + -
55A ARG* 2.9 43.6 + - - +
68A TRP* 3.6 45.8 - - + +
71A GLN* 4.9 0.5 - - - +
353A LEU* 3.7 28.0 - - + -
362A ILE 3.0 14.5 + - - +
364A PHE* 4.0 5.8 - - + -
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Residues in contact with PHE 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 SER 3.5 0.2 - - - -
12A VAL* 1.3 100.1 - - + +
14A GLN* 1.3 66.4 + - - +
20A TYR* 3.9 26.2 - + + -
36A ALA* 3.7 31.9 - - + -
37A PHE 4.4 3.1 - - - -
38A ALA* 3.9 15.0 - - + -
53A VAL* 3.6 18.8 - - + -
54A LEU 4.6 0.2 - - - -
55A ARG* 3.8 22.7 - - + -
71A GLN* 3.3 28.0 - - + -
353A LEU* 5.0 0.9 - - + -
361A GLU* 3.2 4.4 - - - +
362A ILE* 2.9 56.4 + - + +
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Residues in contact with GLN 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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11A SER* 3.8 24.8 + - - +
13A PHE* 1.3 81.0 - - - +
15A SER* 1.3 65.6 + - - +
20A TYR* 3.3 15.8 - - - -
360A GLU 3.5 4.3 - - - -
361A GLU* 3.2 33.9 + - + -
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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