Contacts of the strand formed by residues 17 - 24 (chain B) in PDB entry 5I0X
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 MET 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR* 3.2 5.9 - - - +
14B MET 3.0 40.5 + - - +
15B ASN* 3.2 12.9 - - + +
16B GLU* 1.3 83.5 - - - +
18B GLU* 1.3 59.8 + - - +
19B LEU* 3.6 10.5 - - + +
49B ILE* 3.9 15.7 - - + -
50B HIS 3.2 9.9 - - - +
52B VAL* 4.2 5.2 - - - +
55B ASN* 4.3 3.8 - - - +
65B ILE* 3.7 37.9 - - + -
68B LEU* 4.9 2.2 - - - -
116B ILE* 5.6 0.4 - - + -
138B TRP* 3.5 40.4 - - + -
141B PHE* 3.7 17.0 - - + -
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Residues in contact with GLU 18 (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 PRO* 3.9 24.5 - - + +
12B VAL 3.7 4.9 - - - +
13B THR* 4.2 12.8 + - - +
17B MET* 1.3 73.3 - - - +
19B LEU* 1.3 62.9 + - - +
20B ALA* 5.1 3.1 - - + +
48B ASP 3.4 2.3 - - - +
49B ILE* 3.3 5.2 - - - +
50B HIS* 2.8 34.9 + - + +
52B VAL* 3.9 20.1 - - + +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.5 2.2 - - - +
12B VAL* 2.8 48.3 + - + +
14B MET* 3.8 26.2 - - + +
17B MET* 3.6 19.3 - - + +
18B GLU* 1.3 76.2 - - - +
20B ALA* 1.3 57.8 + - - +
48B ASP 3.3 4.9 - - - -
49B ILE* 3.8 25.8 - - + -
114B TYR* 6.1 0.7 - - + -
116B ILE* 3.3 34.1 - - + -
141B PHE* 4.0 11.9 - - + -
143B VAL* 4.4 4.9 - - + -
145B TYR* 2.8 27.0 + - - +
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Residues in contact with ALA 20 (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 PRO* 4.2 22.9 - - + -
18B GLU* 4.1 4.0 - - + -
19B LEU* 1.3 76.0 - - - +
21B ALA* 1.3 61.8 + - - +
22B VAL* 4.9 4.3 - - + -
47B ALA* 3.5 5.5 - - - +
48B ASP* 2.8 46.3 + - + +
114B TYR* 4.4 1.4 - - - -
145B TYR* 4.1 6.5 + - - -
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Residues in contact with ALA 21 (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 PRO* 3.8 2.4 - - - +
8B ALA* 2.9 36.0 + - + +
10B GLU 6.0 0.4 - - - -
20B ALA* 1.3 76.1 - - - +
22B VAL* 1.3 67.7 + - - +
45B LEU* 5.1 0.2 - - + -
46B GLU 3.4 4.3 - - - -
112B VAL* 5.0 1.1 - - + -
114B TYR* 3.4 21.3 - - + +
145B TYR* 3.8 34.4 - - + -
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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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5B GLU* 4.2 25.1 - - + +
6B TYR 3.3 13.2 - - - +
7B PRO* 5.0 4.0 - - + -
8B ALA 4.2 0.4 - - - +
20B ALA* 4.9 4.7 - - + -
21B ALA* 1.3 82.0 - - - +
23B TYR* 1.3 64.5 + - - +
24B LEU* 4.5 2.0 - - + -
45B LEU* 3.3 8.5 - - - +
46B GLU* 2.9 64.5 + - + +
48B ASP* 3.5 20.2 - - - +
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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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5B GLU* 3.6 1.2 - - - -
6B TYR* 2.8 58.2 + + + +
7B PRO 4.2 8.7 - - - -
8B ALA* 4.4 12.1 - - + -
22B VAL* 1.3 75.6 - - - +
24B LEU* 1.3 66.4 + - - +
43B VAL* 3.8 24.2 - - + -
44B HIS 3.2 13.2 - - - +
45B LEU* 3.9 12.3 - - + -
104B MET* 6.5 0.2 - - + -
147B PHE* 4.0 24.2 - + + -
148B LYS 4.0 14.1 + - - -
149B TYR* 4.2 24.1 - + - -
150B VAL 5.2 1.0 + - - -
151B GLY 5.2 0.9 + - - -
152B LEU* 4.1 24.0 - - + -
158B VAL* 3.7 16.3 - - - +
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Residues in contact with LEU 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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127A HIS* 5.3 3.8 - - + -
132A THR* 5.5 5.6 - - + -
3B PHE* 4.4 17.7 - - + +
4B LYS 3.3 22.2 - - - +
5B GLU* 4.2 20.9 - - + +
6B TYR* 4.9 1.3 - - - -
22B VAL* 4.5 1.1 - - + -
23B TYR* 1.3 80.3 - - - +
25B GLN* 1.3 66.5 + - + +
27B ILE* 3.7 27.8 - - + -
43B VAL* 3.3 8.3 - - - +
44B HIS* 2.7 41.9 + - + +
46B GLU* 3.5 29.8 - - - +
152B LEU* 3.5 11.2 - - - -
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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