Contacts of the strand formed by residues 30 - 34 (chain V) in PDB entry 5L4K
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 GLN 30 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542N GLU* 3.9 20.7 + - - +
771N PHE* 3.4 33.8 - - - -
28V ALA* 3.2 12.2 + - + +
29V GLU* 1.3 76.2 - - - +
31V VAL* 1.3 68.6 + - - +
32V TYR* 3.9 11.0 + - - -
65V TYR 3.2 9.4 + - - +
66V THR* 3.6 11.0 - - + +
67V VAL* 3.0 27.2 + - - +
181V LEU* 4.9 10.1 - - - +
203V ILE* 3.9 0.4 - - - -
204V THR* 3.4 18.3 + - - +
206V ASN* 2.8 28.1 - - - +
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Residues in contact with VAL 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V GLU* 5.6 0.2 - - + -
30V GLN* 1.3 79.2 - - - +
32V TYR* 1.3 70.1 + - - +
33V ILE* 3.7 25.1 + - + -
67V VAL* 3.6 16.6 - - + +
69V VAL* 3.9 18.2 - - + -
141V VAL* 4.0 22.2 - - + -
143V VAL* 4.9 6.3 - - + -
159V ALA* 4.4 0.4 - - + -
203V ILE* 3.7 19.1 - - + -
204V THR 3.2 4.8 + - - -
205V ILE* 3.9 17.3 - - + +
206V ASN* 3.0 27.7 + - - +
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Residues in contact with TYR 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540N GLN* 5.0 8.5 - - + -
541N HIS* 5.2 1.9 - - - -
542N GLU* 3.1 38.2 + - - +
30V GLN* 3.9 6.9 - - - -
31V VAL* 1.3 73.5 - - - +
33V ILE* 1.3 62.0 + - - +
34V SER 4.0 0.4 - - - +
62V VAL* 5.8 0.9 - - + -
66V THR* 3.6 25.2 + - + +
67V VAL 3.0 9.6 + - - +
68V ARG* 3.9 25.8 - - + -
69V VAL* 3.0 30.8 + - - +
206V ASN* 3.5 37.0 - - + -
207V TYR 4.8 5.2 - - - -
208V ARG* 4.2 34.8 - - + +
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Residues in contact with ILE 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V VAL* 3.7 17.8 + - + +
32V TYR* 1.3 77.1 - - - +
34V SER* 1.3 65.3 + - - +
35V SER 3.7 1.0 + - - -
37V ALA* 3.5 26.2 - - + -
38V LEU* 3.7 18.1 - - + +
41V MET* 4.1 13.0 - - + -
57V MET* 6.3 0.7 - - - -
69V VAL* 3.9 10.8 - - + +
143V VAL* 4.6 8.5 - - + -
157V ILE* 3.7 29.8 - - + -
205V ILE* 4.1 26.5 - - + -
206V ASN 4.1 7.4 + - - +
207V TYR* 3.8 27.7 - - + +
208V ARG 4.1 1.6 + - - -
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Residues in contact with SER 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U ASP* 5.7 0.5 + - - -
32V TYR* 4.0 1.4 - - - +
33V ILE* 1.3 75.2 - - - +
35V SER* 1.3 57.0 + - - +
36V LEU* 2.7 19.4 + - - +
37V ALA 2.8 18.2 + - - -
38V LEU* 3.4 6.5 + - - +
69V VAL 3.4 12.6 + - - -
70V ILE* 3.0 33.3 + - - +
208V ARG* 4.9 24.9 - - - +
213V GLU* 5.1 4.5 - - - -
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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