Contacts of the strand formed by residues 21 - 29 (chain B) in PDB entry 2IJO
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 GLY 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ARG* 3.8 6.7 - - - -
58A ALA 3.7 9.9 - - - -
60A ILE* 4.0 15.7 - - - -
19B THR 3.4 1.4 + - - -
20B THR* 1.3 77.6 - - - +
22B VAL* 1.3 64.1 + - - -
23B TYR* 3.4 7.6 - - - -
40B VAL* 3.4 2.9 - - - +
41B MET* 2.7 39.4 + - - +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG* 3.5 3.3 - - - -
57A THR* 2.8 35.1 + - + +
58A ALA* 3.0 15.5 + - + +
59A ASP 3.8 21.8 - - - +
60A ILE* 4.0 13.7 - - + -
21B GLY* 1.3 73.9 - - - -
23B TYR* 1.3 63.7 + - - +
39B GLY 3.7 10.3 - - - +
40B VAL* 4.6 0.9 - - + +
98B ILE* 4.1 17.0 - - + -
100B VAL* 3.6 30.1 - - + -
106B VAL* 4.9 1.3 - - + -
138B PRO* 4.2 18.6 - - + -
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.7 23.1 - - + -
55A GLU* 3.3 14.8 - - - -
56A ARG* 3.1 38.4 - - + +
57A THR* 4.2 2.5 - - - -
17B ASP* 3.3 22.8 + - - -
18B THR 4.2 0.9 - - - -
19B THR* 2.6 35.9 + - - -
21B GLY 3.4 14.4 - - - -
22B VAL* 1.3 79.5 - - - +
24B ARG* 1.3 65.5 + - - +
38B ALA* 3.1 25.1 - - - +
39B GLY 2.9 13.2 + - - +
41B MET* 3.4 25.4 - - + +
46B PHE* 3.7 22.0 - + + -
60B SER* 4.7 2.0 - - - -
100B VAL* 4.3 2.1 - - - +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.3 6.9 - - - +
55A GLU* 3.1 38.4 + - + +
57A THR* 3.2 32.1 + - + -
23B TYR* 1.3 74.6 - - - +
25B ILE* 1.3 61.6 + - - +
26B MET* 3.7 21.3 + - + +
35B GLN* 2.7 39.7 + - - +
37B GLY 3.6 4.5 - - - -
38B ALA* 4.3 0.2 - - - +
100B VAL* 3.5 21.8 - - + +
101B GLU 3.2 19.0 + - - -
102B PRO* 4.5 0.8 - - - +
103B GLY* 4.5 3.1 - - - +
104B ARG 2.7 24.0 + - - -
105B ASN* 4.1 11.3 - - - +
106B VAL* 4.1 6.3 - - - +
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A MET* 4.0 26.9 - - + -
53A TRP 3.6 3.1 - - - -
54A ILE* 4.4 2.5 - - + -
24B ARG* 1.3 74.3 - - - +
26B MET* 1.3 55.9 + - - +
35B GLN* 3.5 2.9 - - - -
36B ALA* 2.7 33.6 + - + -
37B GLY 2.8 16.3 + - - +
38B ALA* 3.2 35.9 - - - +
46B PHE* 3.9 24.5 - - + -
48B THR* 3.5 13.7 - - - +
52B THR* 3.6 15.3 - - - +
53B THR* 4.0 15.9 - - + -
58B LEU* 4.3 10.5 - - + -
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A MET* 3.1 12.1 - - - +
53A TRP* 2.8 66.8 + - + +
55A GLU* 3.8 24.0 - - + +
24B ARG* 4.1 21.5 - - - +
25B ILE* 1.3 75.3 - - - +
27B THR* 1.3 63.0 + - - +
33B SER* 4.7 8.1 - - - +
34B TYR* 3.4 31.2 - - - +
35B GLN* 3.6 22.2 - - + +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 2.9 27.1 + - - +
52A MET* 3.8 18.9 - - + +
53A TRP* 3.7 7.9 - - - -
26B MET* 1.3 76.3 - - - +
28B ARG* 1.3 66.8 + - - +
33B SER* 3.4 5.0 + - - -
34B TYR* 2.9 71.1 + - + +
36B ALA* 4.2 10.1 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.9 4.4 + - - +
53A TRP* 3.8 14.1 - - + -
27B THR* 1.3 82.3 + - - +
29B GLY* 1.3 65.4 + - - +
30B LEU 5.4 2.0 + - - -
32B GLY* 3.5 27.2 - - - +
33B SER* 3.7 31.3 - - - +
34B TYR* 4.2 3.5 - - - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 1.3 85.4 + - - +
30B LEU* 1.3 59.6 + - - -
31B LEU 2.7 14.5 + - - -
32B GLY 2.6 20.9 + - - +
34B TYR* 3.8 16.2 - - - -
19I ILE* 5.9 3.6 - - - -
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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