Contacts of the strand formed by residues 51 - 60 (chain B) in PDB entry 4ICX
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 GLU 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LEU 3.7 11.2 - - - +
16B GLU* 3.8 13.5 - - - +
44B VAL* 3.2 26.4 - - - +
45B ASP 4.9 0.4 + - - -
49B GLN 3.5 3.9 + - - +
50B PRO* 1.3 73.4 - - - +
52B PHE* 1.3 60.8 + - - +
53B ALA* 3.5 23.9 - - + +
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Residues in contact with PHE 52 (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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14B ILE* 3.4 31.9 - - + +
15B LEU 3.0 6.4 + - - +
16B GLU* 4.0 10.1 - - - -
17B GLY 4.0 6.1 - - - -
28B LEU* 3.8 34.1 - - + -
30B VAL* 3.6 29.8 - - + -
41B THR* 4.4 13.0 - - + -
44B VAL* 3.7 28.4 - - + +
50B PRO* 3.9 27.1 - - + -
51B GLU* 1.3 74.1 - - - +
53B ALA* 1.3 74.8 + - - +
54B THR* 2.8 17.6 + - - +
79B CYS* 5.2 0.2 - - - -
126B ILE* 4.2 17.9 - - + -
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Residues in contact with ALA 53 (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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14B ILE 3.0 10.1 + - - -
15B LEU* 3.0 15.9 + - - +
51B GLU* 3.5 22.2 - - + +
52B PHE* 1.3 74.8 - - - +
54B THR* 1.3 58.1 + - - +
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Residues in contact with THR 54 (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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12B VAL 3.6 1.6 - - - +
13B SER* 3.4 2.4 - - - -
14B ILE* 2.8 42.8 + - - +
15B LEU* 5.7 0.8 - - - +
40B ALA 5.2 0.4 - - - +
41B THR* 4.0 30.9 - - + +
42B ASP* 5.0 3.8 + - - +
52B PHE* 2.8 22.1 + - - -
53B ALA* 1.3 72.9 + - - +
55B GLU* 1.3 75.5 + - - +
56B LEU* 4.0 18.2 - - + -
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Residues in contact with GLU 55 (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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11B VAL* 3.8 22.2 - - + +
12B VAL 3.4 3.1 - - - -
13B SER* 3.5 21.8 + - - +
54B THR* 1.3 79.9 - - - +
56B LEU* 1.3 67.8 + - - +
57B ALA* 4.3 2.2 + - + +
133B GLU* 4.9 5.5 - - - +
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Residues in contact with LEU 56 (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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10B ILE 3.6 1.6 - - - +
11B VAL* 3.4 2.6 - - - -
12B VAL* 2.8 44.9 + - + +
14B ILE* 3.7 25.4 - - + -
30B VAL 4.8 1.3 - - - +
32B ALA* 3.6 30.1 - - + +
39B LEU* 4.1 20.4 - - + +
40B ALA 3.8 24.7 - - - +
41B THR* 4.4 6.3 - - + -
54B THR* 4.0 14.6 - - + +
55B GLU* 1.3 82.2 - - - +
57B ALA* 1.3 60.5 + - - +
58B TRP* 3.8 18.4 - - + -
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Residues in contact with ALA 57 (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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9B LEU* 4.5 18.8 - - + -
10B ILE 3.3 7.2 - - - +
11B VAL* 4.5 15.7 - - + -
37B GLU* 4.6 4.0 - - - +
39B LEU* 3.3 18.8 - - - +
55B GLU* 4.2 2.2 + - + +
56B LEU* 1.3 74.9 - - - +
58B TRP* 1.3 63.6 + - - +
59B GLU 4.3 0.2 - - - -
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Residues in contact with TRP 58 (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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9B LEU* 3.4 8.2 - - - -
10B ILE* 3.0 53.7 + - + +
12B VAL* 3.7 26.9 - - + -
32B ALA* 3.6 43.1 - - + -
34B PHE* 3.8 36.9 - + + +
37B GLU* 3.0 51.7 + - + +
39B LEU* 3.4 22.4 - - + +
56B LEU* 3.8 15.7 - - + -
57B ALA* 1.3 74.3 - - - +
59B GLU* 1.3 66.4 + - - +
60B ILE* 3.6 1.4 + - - +
75B ILE* 4.0 13.9 - - + -
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Residues in contact with GLU 59 (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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7B GLN* 5.8 4.0 - - + +
8B LEU 3.8 1.1 - - - +
9B LEU* 3.6 22.4 - - + -
37B GLU* 5.0 8.9 + - - +
57B ALA 4.3 0.6 + - - -
58B TRP* 1.3 73.6 - - - +
60B ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 60 (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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7B GLN* 3.5 4.1 - - - +
8B LEU* 2.9 64.7 + - + +
10B ILE* 4.1 25.4 - - + -
34B PHE* 3.9 16.4 - - + -
35B ASP* 5.6 1.1 - - - +
58B TRP 4.4 0.9 - - - +
59B GLU* 1.3 78.3 - - - +
61B ASP* 1.3 72.8 + - - +
64B ALA* 4.1 9.4 - - + -
65B LEU* 4.1 13.5 - - + +
68B HIS* 3.5 32.1 - - + +
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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