Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 1W7I
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 VAL 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASP* 3.7 14.2 - - - +
36A LYS* 1.3 91.7 - - + +
38A LEU* 1.3 66.1 + - - +
39A GLN* 3.4 23.7 + - - +
49A GLU* 4.7 14.6 - - + +
50A TYR 3.2 13.9 - - - +
51A CYS* 4.1 21.8 - - + -
52A LEU* 4.7 2.2 - - - -
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Residues in contact with LEU 38 (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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7A TYR* 5.1 6.5 - - + -
13A VAL* 5.7 0.9 - - + -
27A LEU* 4.9 11.7 - - + -
31A TYR* 3.6 45.5 - - + -
37A VAL* 1.3 74.3 - - - +
39A GLN* 1.3 64.8 + - - +
40A LEU* 4.0 21.5 - - + -
49A GLU* 3.4 6.2 - - - -
50A TYR* 2.9 41.1 + - + +
52A LEU* 4.1 8.9 - - + +
59A LEU* 4.1 10.1 - - + -
60A PRO* 3.7 37.5 - - + -
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Residues in contact with GLN 39 (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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26A GLU 3.5 0.5 - - - +
27A LEU* 3.6 3.2 - - - +
28A LEU* 2.6 56.5 + - + +
29A LYS* 4.3 20.1 + - + +
37A VAL* 3.4 28.5 + - - +
38A LEU* 1.3 86.2 + - - +
40A LEU* 1.3 57.1 + - - +
48A LEU 4.0 5.3 - - - +
49A GLU* 3.7 19.0 + - - +
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Residues in contact with LEU 40 (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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13A VAL* 4.2 10.5 - - + -
15A ILE* 3.8 28.5 - - + -
25A ALA* 3.9 17.3 - - + -
26A GLU 3.1 23.8 - - - +
27A LEU* 4.0 16.4 - - + -
28A LEU* 3.5 12.3 - - - +
38A LEU* 4.0 12.3 - - + -
39A GLN* 1.3 77.8 - - - +
41A ARG* 1.3 61.1 + - - +
42A LEU* 5.2 0.9 - - + -
47A ASP 3.7 13.9 + - - -
48A LEU* 3.2 31.2 + - + +
50A TYR* 3.4 35.2 - - + -
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Residues in contact with ARG 41 (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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24A SER* 4.1 0.9 + - - +
25A ALA* 3.4 6.2 - - - -
26A GLU* 3.1 38.6 + - + +
28A LEU* 4.2 13.2 - - + -
40A LEU* 1.3 78.3 - - - +
42A LEU* 1.3 64.6 + - - +
45A GLY 3.8 4.7 - - - -
46A LYS* 3.8 20.9 - - + +
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Residues in contact with LEU 42 (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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15A ILE* 3.8 24.0 - - + -
23A LYS* 5.3 6.3 - - + -
24A SER 3.1 25.6 - - - +
25A ALA* 3.9 7.0 - - + -
40A LEU* 5.2 0.4 - - + -
41A ARG* 1.3 78.6 - - - +
43A GLU* 1.4 56.9 + - - +
44A GLU* 3.0 4.3 + - + -
45A GLY* 2.9 35.6 + - - +
47A ASP* 4.3 21.5 - - - +
48A LEU* 4.0 23.8 - - + -
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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