Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 4WCI
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 TRP 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 3.5 25.6 - + - -
17A GLU* 3.6 26.0 - - + -
31A LYS* 3.7 12.5 - - - +
32A LEU 5.1 0.7 + - - -
34A GLU* 3.6 22.4 - - + +
35A GLU 3.1 15.5 - - - +
36A GLY* 1.3 86.0 - - - +
38A LEU* 1.3 69.0 + - - +
48A MET* 3.9 25.8 - - + +
49A PHE* 3.2 32.3 - - - -
50A PRO* 3.4 33.4 - - + -
51A ASP* 5.0 0.7 - - - +
385B ALA* 4.1 6.1 - - + -
386B PRO* 2.9 31.8 + - + +
387B PRO 3.6 9.0 + - - -
388B ARG* 3.3 25.0 - - + +
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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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4A TYR* 3.5 42.4 - - + +
29A VAL* 3.9 7.0 - - + -
30A LYS 3.8 15.0 - - - +
31A LYS* 3.9 22.9 - - + +
32A LEU 5.5 0.7 - - - +
37A TRP* 1.3 81.0 - - - +
39A GLU* 1.3 61.2 + - - +
48A MET* 3.2 11.6 - - - +
49A PHE* 2.9 54.7 + - + -
51A ASP* 3.8 24.0 - - + +
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Residues in contact with GLU 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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29A VAL* 3.2 4.5 - - - +
30A LYS* 2.8 47.4 + - - +
32A LEU* 3.7 24.4 - - + +
38A LEU* 1.3 75.2 - - - +
40A GLY* 1.3 58.8 + - - +
46A ARG* 2.8 61.1 + - - +
47A GLY* 3.4 10.6 + - - +
48A MET* 3.5 22.9 - - - -
49A PHE* 3.6 3.8 - - - -
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Residues in contact with GLY 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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18A LEU* 4.1 3.6 - - - +
26A ILE* 3.8 15.7 - - - -
27A ARG 3.6 9.0 - - - -
28A ASN 4.1 0.2 - - - -
29A VAL* 4.3 1.1 - - - -
39A GLU* 1.3 78.2 - - - +
41A GLU* 1.3 61.4 + - - -
42A LEU 4.0 0.2 + - - -
46A ARG* 3.2 16.2 - - - -
47A GLY 3.0 33.5 + - - +
49A PHE* 3.6 2.4 - - - -
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Residues in contact with GLU 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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25A ILE 4.3 0.9 - - - +
26A ILE* 3.5 4.0 - - - -
27A ARG* 2.8 56.6 + - + +
40A GLY* 1.3 71.5 - - - -
42A LEU* 1.3 65.6 + - - +
43A ASN 3.4 3.1 + - - -
44A GLY* 2.7 34.5 + - - -
45A ARG 3.3 12.6 - - - +
46A ARG* 3.9 13.8 - - + +
21C ARG* 4.5 10.1 - - + -
22C VAL 3.7 23.1 - - - +
24C GLU* 3.3 28.6 + - + +
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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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18A LEU* 3.8 22.9 - - + -
19A THR 3.9 16.4 - - - +
20A ILE* 4.0 14.8 - - + -
24A GLU* 3.4 36.6 - - + +
25A ILE 3.5 24.2 - - - +
26A ILE* 4.4 5.8 - - + -
40A GLY 4.0 0.4 + - - -
41A GLU* 1.3 76.5 - - - +
43A ASN* 1.3 93.7 + - + +
44A GLY 3.1 1.7 + - - -
45A ARG* 2.8 28.7 + - - +
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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