Contacts of the strand formed by residues 38 - 42 (chain C) in PDB entry 1QA7
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 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLY* 3.6 4.3 - - - -
34C VAL* 3.1 34.3 + - + +
35C LYS* 2.9 18.4 + - + +
36C ASP* 4.5 12.6 - - + -
37C ASP* 1.3 78.9 - - - +
39C LEU* 1.3 63.5 + - - +
74C VAL* 3.6 24.7 - - + -
76C GLN* 4.1 9.6 - - + -
87C LEU* 3.8 20.2 - - + -
88C MET 3.3 29.2 - - - -
89C LYS* 3.3 59.6 - - + +
96C PHE* 4.3 1.2 - - - -
212C ILE* 3.6 45.9 + - + +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 4.8 6.1 - - + -
31C ALA* 4.7 2.5 - - + -
32C LEU 3.2 7.0 - - - +
33C GLY* 3.9 6.1 - - - +
34C VAL* 4.3 3.6 - - - -
37C ASP 4.5 0.7 - - - +
38C TRP* 1.3 76.0 - - - +
40C LEU* 1.3 64.1 + - - +
41C VAL* 3.5 14.2 + - + +
59C PHE* 3.1 41.3 - - + -
87C LEU* 3.3 6.0 - - - -
88C MET* 2.9 36.6 + - + +
90C VAL* 3.2 27.1 - - + -
93C ILE* 4.5 3.1 - - + -
96C PHE* 3.3 39.0 - - + -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA* 3.5 5.9 - - - -
32C LEU* 2.6 37.9 + - + +
34C VAL* 3.6 18.4 - - + +
39C LEU* 1.3 72.0 - - - +
41C VAL* 1.3 59.4 + - - +
42C PRO* 4.3 2.3 - - - +
78C LEU* 4.2 14.1 - - + -
85C VAL* 4.3 11.2 - - + -
86C VAL 3.6 4.9 - - - +
87C LEU* 3.0 33.0 - - + -
103C PHE* 3.5 37.7 - - + -
173C GLY 5.4 0.3 - - - +
190C ILE* 3.8 30.3 - - + +
204C VAL* 4.2 9.6 - - + -
209C PHE* 4.5 0.9 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 4.1 30.1 - - + -
30C ASN 4.8 0.4 - - - +
31C ALA* 4.0 10.8 - - + -
39C LEU* 3.8 24.9 - - + +
40C LEU* 1.3 78.0 - - - +
42C PRO* 1.3 82.6 - - + +
43C SER 3.3 1.2 + - - -
45C ALA* 4.5 3.1 - - + -
46C TYR* 4.8 2.7 - - + -
59C PHE* 4.8 2.2 - - + -
85C VAL* 4.0 4.0 - - - +
86C VAL* 2.7 42.5 + - + +
88C MET* 4.0 30.5 - - + -
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Residues in contact with PRO 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET* 3.5 26.7 - - - -
30C ASN 4.0 9.4 - - - +
40C LEU 4.3 2.0 - - - +
41C VAL* 1.3 93.3 - - + +
43C SER* 1.3 59.8 + - - +
44C HIS* 3.1 22.7 - - + +
45C ALA* 3.0 29.1 - - - +
46C TYR* 4.2 0.2 - - - -
84C ASP 3.4 7.9 - - - +
85C VAL* 3.8 3.8 - - + -
173C GLY* 3.8 20.9 - - - +
190C ILE* 3.9 14.1 - - + -
191C HIS 4.4 3.4 - - - +
192C VAL* 4.4 5.6 - - + -
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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
------------------------------------------------------------
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