Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 6JBQ
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 HIS 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLU* 5.3 1.1 - - - -
18A GLN* 3.6 13.8 - - - +
19A VAL* 3.6 32.3 - - + +
20A SER* 3.1 29.2 + - - +
22A THR* 1.3 78.7 - - - +
24A ALA* 1.3 88.9 + - - +
25A LYS* 4.3 14.4 - - + +
182A ARG* 3.3 25.8 - - - -
204A GLU* 4.9 6.8 + - + +
205A MET 3.7 4.6 + - - -
206A GLU* 2.7 34.0 + - + +
213A PRO* 4.7 2.7 - - - +
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Residues in contact with ALA 24 (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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16A ILE* 5.2 6.5 - - + -
17A GLU 3.7 6.5 - - - +
18A GLN* 4.7 2.5 - - + +
22A THR 4.2 0.2 + - - -
23A HIS* 1.3 81.8 + - - +
25A LYS* 1.3 62.2 + - - +
26A VAL* 4.1 12.6 - - + -
203A ILE 3.9 0.9 - - - +
204A GLU* 3.8 2.4 - - - -
205A MET* 3.2 39.8 + - + +
213A PRO* 3.8 29.8 - - + +
217A ILE* 6.2 0.4 - - + -
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Residues in contact with LYS 25 (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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15A ASP 4.4 0.5 - - - +
17A GLU* 2.7 57.4 + - + +
23A HIS* 4.3 12.3 - - - +
24A ALA* 1.3 75.0 - - - +
26A VAL* 1.3 61.0 + - - +
27A THR* 4.2 2.6 + - - +
202A VAL* 4.1 28.0 - - + -
203A ILE 3.6 3.6 - - - -
204A GLU* 4.4 19.8 + - + -
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Residues in contact with VAL 26 (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* 6.1 2.7 - - + -
15A ASP 3.7 5.2 - - - +
16A ILE* 3.8 41.3 - - + -
24A ALA* 5.1 6.7 - - + -
25A LYS* 1.3 78.6 - - - +
27A THR* 1.3 59.4 + - - +
28A LEU* 5.8 1.6 - - + -
202A VAL* 3.7 3.2 - - - +
203A ILE* 2.8 51.8 + - + +
205A MET* 6.2 0.2 - - + -
213A PRO 6.2 0.2 - - - +
217A ILE* 3.8 29.8 - - + -
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Residues in contact with THR 27 (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* 3.7 14.4 - - - +
15A ASP* 3.4 41.0 + - - +
25A LYS* 5.4 1.6 - - - +
26A VAL* 1.3 77.1 - - - +
28A LEU* 1.3 65.4 + - - +
200A LYS* 2.9 38.3 + - - +
201A LEU 3.3 13.0 + - - -
202A VAL* 4.1 10.1 - - - -
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Residues in contact with LEU 28 (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 PRO* 4.0 15.5 - - + -
14A VAL* 3.8 20.4 - - + -
26A VAL* 5.4 1.8 - - + +
27A THR* 1.3 77.5 + - - +
29A GLU* 1.3 63.8 + - - +
31A LEU* 3.6 28.8 - - + +
39A LEU* 5.7 5.4 - - + -
200A LYS* 4.0 1.2 - - - +
201A LEU* 3.1 62.2 + - + +
203A ILE* 4.6 11.0 - - + -
231B PHE* 4.9 20.4 - - + -
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Residues in contact with GLU 29 (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 PRO* 3.8 14.2 - - - +
12A ARG 5.1 0.5 + - - -
13A LEU 4.8 8.0 + - - +
14A VAL* 5.0 0.8 - - - +
27A THR* 5.0 0.2 - - - +
28A LEU* 1.3 78.4 - - - +
30A PRO* 1.3 74.6 - - + +
190A ALA* 5.2 2.7 - - + -
199A ASP 4.9 0.9 - - - -
200A LYS* 3.9 31.6 - - + -
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Residues in contact with PRO 30 (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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9A LEU* 4.1 16.4 - - + +
10A LYS 4.3 4.3 - - - +
11A PRO* 3.9 22.2 - - + +
29A GLU* 1.3 87.0 - - + +
31A LEU* 1.3 69.3 + - - +
190A ALA* 4.8 7.4 - - + -
191A ARG 5.4 6.5 - - - +
192A VAL* 5.2 11.2 - - + -
198A LEU* 3.7 24.5 - - + -
199A ASP 4.2 2.5 - - - +
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Residues in contact with LEU 31 (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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9A LEU* 4.6 6.5 - - - -
11A PRO* 4.4 7.4 - - + -
28A LEU* 3.6 49.4 - - + +
29A GLU* 4.2 0.4 - - - +
30A PRO* 1.3 80.1 - - - +
32A GLU* 1.3 70.8 + - - +
35A PHE* 4.1 9.4 - - + +
36A GLY* 3.9 30.3 - - - +
39A LEU* 4.3 14.1 - - + -
198A LEU* 3.3 16.7 - - - +
199A ASP* 3.1 34.0 + - + +
201A LEU* 5.0 7.2 - - + +
227B GLN* 4.7 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