Contacts of the strand formed by residues 32 - 36 (chain A) in PDB entry 1L0V
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.3 33.9 - - + +
9A ILE* 4.6 16.6 - - + -
20A ALA* 3.7 9.9 - - + +
23A ALA* 3.5 30.1 - - + +
24A ALA* 3.5 25.6 - - + +
30A ALA* 4.2 7.4 - - + -
31A LYS* 1.3 75.3 - - - +
33A ALA* 1.3 65.5 + - - +
34A LEU* 3.6 1.7 + - - +
148A GLN* 2.8 18.5 + - + +
149A ILE* 3.4 13.6 - - + -
150A GLN* 2.6 35.4 + - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 4.1 18.2 - - + -
7A LEU 3.0 9.7 + - - +
8A ALA* 3.4 3.7 - - + -
9A ILE 2.8 28.1 + - - +
31A LYS* 3.9 3.7 + - - +
32A ILE* 1.3 73.0 - - - +
34A LEU* 1.3 61.3 + - - +
35A ILE* 3.7 2.2 + - + +
150A GLN* 3.3 7.0 - - - -
152A PHE* 3.7 23.3 - - + -
183A ILE* 4.2 17.0 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.7 21.3 - - + -
11A GLY 3.4 24.9 - - - +
12A ALA* 4.0 15.7 - - + -
16A GLY 4.0 8.7 - - - +
17A LEU* 3.8 29.2 - - + -
20A ALA* 4.4 12.1 - - + -
32A ILE* 3.6 2.3 + - + -
33A ALA* 1.3 72.3 - - - +
35A ILE* 1.3 57.6 + - - +
36A SER* 5.6 0.4 + - - +
143A SER* 5.6 0.9 - - - +
149A ILE* 3.8 19.3 - - + -
150A GLN 2.9 6.9 + - - -
151A ARG* 3.3 24.3 - - + +
152A PHE* 2.8 31.9 + - - +
153A ASP* 5.4 0.2 - - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.5 4.7 - - + -
9A ILE 2.7 16.3 + - - +
10A VAL* 3.6 1.2 - - - -
11A GLY* 2.6 37.2 + - - -
33A ALA 4.0 10.8 - - - +
34A LEU* 1.3 79.2 - - - +
36A SER* 1.3 62.4 + - - +
152A PHE* 3.9 7.6 - - + +
155A HIS* 3.4 37.5 - - + +
157A VAL* 3.7 18.4 - - + -
170A LEU* 3.8 29.6 - - + -
172A ALA* 4.9 1.8 - - + -
183A ILE* 3.5 31.4 - - + -
703A FAD 4.5 0.9 - - - -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.5 20.6 - - - +
34A LEU* 5.6 0.5 + - - +
35A ILE* 1.3 78.9 - - - +
37A LYS* 1.3 58.2 + - - +
38A VAL 2.8 21.4 + - - -
40A PRO* 4.1 6.9 - - - +
152A PHE 3.5 3.3 + - - +
153A ASP* 4.6 5.2 + - - -
154A GLU 2.9 24.8 + - - -
155A HIS 3.0 9.1 + - - -
703A FAD 3.3 35.2 - - - -
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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