Contacts of the strand formed by residues 36 - 44 (chain B) in PDB entry 4KJI
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 ILE 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 3.8 1.2 - - - +
16A LEU* 2.9 58.2 + - + +
16B LEU* 3.7 20.9 - - + -
31B LEU* 4.3 21.1 - - + -
35B GLY* 1.3 76.6 - - - +
37B ARG* 1.3 61.9 + - - +
38B ILE* 4.2 5.4 - - + -
52B ILE* 3.2 35.2 - - + -
53B GLU 3.4 11.4 - - - +
54B ALA* 3.8 14.6 - - + -
55B PRO* 5.2 0.9 - - + -
58B VAL* 5.6 5.4 - - + -
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Residues in contact with ARG 37 (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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14A ILE 3.7 2.2 - - - +
15A THR* 3.5 21.0 + - + +
63A ASP* 4.4 19.5 + - - +
3B PHE* 5.0 17.1 - - + -
34B GLY 5.5 6.3 - - - +
35B GLY 4.2 0.4 + - - -
36B ILE* 1.3 72.7 - - - +
38B ILE* 1.3 66.4 - - - +
39B LEU* 4.2 12.0 - - + +
51B GLY 4.3 0.2 - - - -
52B ILE* 3.2 7.6 - - - +
53B GLU* 2.9 61.1 + - + +
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Residues in contact with ILE 38 (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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12A GLU 4.3 0.2 - - - +
13A GLY* 3.2 3.4 - - - -
14A ILE* 2.8 52.9 + - + +
16A LEU* 4.0 29.2 - - + -
38A ILE* 3.8 34.1 - - + -
50A VAL* 6.0 4.9 - - + -
52A ILE* 4.5 16.2 - - + -
36B ILE* 4.2 10.5 - - + -
37B ARG* 1.3 81.0 - - - +
39B LEU* 1.3 62.2 + - - +
40B VAL* 4.1 2.1 + - + +
50B VAL* 4.0 20.4 - - + -
51B GLY 3.2 9.0 - - - +
52B ILE* 4.4 4.3 - - + -
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Residues in contact with LEU 39 (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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11A GLY* 3.2 33.0 - - - +
12A GLU 3.7 13.7 - - - +
13A GLY* 3.9 5.4 - - - +
63A ASP* 5.4 2.2 - - - +
3B PHE* 3.6 20.1 - - + -
37B ARG* 4.2 10.9 - - + +
38B ILE* 1.3 77.0 - - - +
40B VAL* 1.3 59.7 + - - +
41B THR* 4.3 13.2 - - + +
50B VAL* 3.4 6.8 - - - +
51B GLY* 2.6 40.8 + - - +
11D U 3.4 41.1 - - + +
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Residues in contact with VAL 40 (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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8A ARG* 3.3 28.5 - - + -
9A ARG 3.6 7.9 - - - +
10A GLU* 3.8 1.1 - - - -
11A GLY* 2.9 25.3 + - - -
12A GLU 3.1 20.5 + - - +
48A ALA* 4.1 23.1 - - + -
50A VAL* 5.9 6.1 - - + -
38B ILE* 5.2 2.0 - - + +
39B LEU* 1.3 71.2 - - - +
41B THR* 1.3 62.4 + - - +
42B ASP 4.5 0.9 - - - +
43B ILE* 4.2 16.6 - - + -
48B ALA* 4.9 3.8 - - + -
49B ARG 3.4 12.1 - - - +
50B VAL* 4.5 11.2 - - + +
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Residues in contact with THR 41 (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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10A GLU* 4.4 3.6 - - - +
11A GLY* 3.7 12.0 + - - +
5B ILE* 3.6 31.0 - - + +
39B LEU* 3.4 10.9 - - + -
40B VAL* 1.3 77.5 - - - +
42B ASP* 1.3 69.4 + - - +
49B ARG* 3.0 28.5 + - - +
50B VAL 4.1 0.2 + - - -
51B GLY* 4.1 11.0 - - - +
11D U 3.7 37.7 - - + +
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Residues in contact with ASP 42 (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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10A GLU* 3.0 22.2 - - - +
40B VAL 5.0 0.9 - - - -
41B THR* 1.3 86.9 + - - +
43B ILE* 1.3 74.7 + - - +
44B ILE* 2.8 32.6 + - - +
49B ARG* 2.8 45.6 + - + +
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Residues in contact with ILE 43 (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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8A ARG 4.5 1.1 - - - +
10A GLU* 2.8 41.7 - - + +
43A ILE* 4.4 19.7 - - + -
45A GLY 3.7 20.4 - - - +
46A ASN* 3.3 19.3 - - - +
47A GLN 4.0 0.2 - - - -
48A ALA* 3.3 43.1 - - + +
40B VAL* 4.2 12.3 - - + -
42B ASP* 1.3 84.8 + - - +
44B ILE* 1.3 73.4 + - - +
45B GLY 4.8 1.3 - - - +
47B GLN 4.1 6.3 - - - +
48B ALA* 5.0 3.1 - - - -
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Residues in contact with ILE 44 (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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42B ASP* 2.8 27.6 - - - +
43B ILE* 1.3 76.5 - - - +
45B GLY* 1.3 61.1 + - - +
46B ASN* 2.9 12.1 + - - +
47B GLN* 3.1 31.4 + - + +
49B ARG* 4.0 23.6 - - - +
1D C 4.0 21.2 - - + +
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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