Contacts of the strand formed by residues 18 - 24 (chain B) in PDB entry 3O7O
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 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.4 4.7 - - - -
15B TRP 3.0 34.9 + - - +
16B ASN* 3.7 11.0 - - + +
17B GLY* 1.3 77.9 - - - +
19B PRO* 1.4 67.5 - - + +
20B LEU* 3.6 19.5 + - + +
71B TYR* 3.7 25.4 - - + -
250B PHE* 4.0 14.8 - - + +
251B SER* 3.8 30.5 - - - -
252B ILE* 3.8 27.8 - - + +
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Residues in contact with PRO 19 (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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13B PHE 3.6 6.1 - - - +
14B VAL* 4.6 9.6 - - + -
17B GLY 3.9 7.4 - - - +
18B ILE* 1.4 86.1 - - + +
20B LEU* 1.4 58.2 + - - +
71B TYR* 3.2 36.1 - - + +
72B GLY 5.1 0.5 + - - -
81B ALA* 3.9 12.9 - - + +
82B GLU 3.1 28.0 - - - +
83B GLY* 3.7 21.8 - - - +
84B SER* 4.0 4.1 - - - +
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Residues in contact with LEU 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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12B ASP* 3.2 6.6 - - - +
13B PHE* 2.8 72.1 + - + +
15B TRP* 3.8 28.5 - - + -
18B ILE* 3.8 12.1 - - + +
19B PRO* 1.4 79.4 - - - +
21B SER* 1.3 63.4 + - - +
69B PHE* 4.1 7.6 - - + -
70B TYR 3.4 17.7 - - - +
71B TYR* 3.7 18.8 - - + +
81B ALA* 3.8 5.8 - - - +
250B PHE* 3.8 27.6 - - + -
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Residues in contact with SER 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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10B THR* 4.2 3.1 - - - -
11B SER 3.4 5.8 - - - -
12B ASP* 2.7 21.5 + - - -
13B PHE* 3.9 2.9 - - - -
20B LEU* 1.3 74.4 - - - +
22B MET* 1.3 60.0 + - - +
69B PHE* 3.1 3.8 - - - +
70B TYR* 2.7 71.2 + - - -
79B HIS* 3.2 13.1 + - - -
81B ALA 3.7 8.5 + - - -
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Residues in contact with MET 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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3B VAL* 3.8 27.4 - - + +
5B MET* 4.3 12.7 - - - +
9B GLY 3.9 0.3 - - - +
10B THR* 3.2 6.6 - - - +
11B SER* 2.7 49.3 + - - +
13B PHE* 3.7 19.9 - - + -
21B SER* 1.3 72.6 - - - +
23B GLU* 1.3 60.1 + - - +
24B LEU 4.2 0.2 - - - -
38B MET* 3.8 26.9 - - - +
40B PHE* 3.3 37.0 - - + +
45B ILE* 3.6 21.5 - - + -
68B GLU 3.6 4.3 - - - +
69B PHE* 4.1 0.4 - - - +
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Residues in contact with GLU 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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9B GLY* 3.4 9.3 + - - +
10B THR* 3.3 20.6 + - - +
21B SER 4.2 0.4 - - - -
22B MET* 1.3 74.9 - - - +
24B LEU* 1.4 59.8 + - - +
25B ASN* 2.9 39.5 + - + +
38B MET* 3.5 3.7 - - - +
68B GLU* 2.8 45.0 + - + +
70B TYR* 4.4 9.7 - - + -
74B LYS* 2.7 32.9 + - - +
77B GLU* 3.7 20.6 - - - +
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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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5B MET* 3.6 35.5 - - + +
7B LYS 3.7 26.9 - - - +
8B PRO* 3.2 28.9 - - + +
9B GLY 3.0 14.1 + - - +
22B MET 4.2 0.2 - - - -
23B GLU* 1.4 67.4 - - - +
25B ASN* 1.3 57.5 + - - +
26B LEU* 3.6 19.7 + - + -
36B VAL* 3.8 33.7 - - + -
37B ALA 4.3 0.2 - - - +
38B MET* 3.9 22.8 - - + +
47B PHE* 3.8 18.6 - - + -
67B PRO* 4.8 0.9 - - + -
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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