Contacts of the strand formed by residues 30 - 34 (chain A) in PDB entry 3Q8L
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 LYS 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLY 3.8 7.2 + - - +
29A ARG* 1.3 75.6 - - - +
31A VAL* 1.3 67.5 + - - +
80A LYS* 3.2 28.5 - - + +
171A LYS 4.1 13.2 - - - +
172A VAL* 4.0 16.6 - - + -
173A TYR* 2.8 30.9 + - - +
296A LEU* 5.7 2.3 + - + -
298A TRP* 3.9 34.1 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 6.1 1.3 - - + -
29A ARG* 4.9 7.9 - - + +
30A LYS* 1.3 82.4 - - - +
32A ALA* 1.3 60.8 + - - +
33A ILE* 4.2 9.9 - - + -
79A ILE* 4.0 22.2 - - + -
80A LYS 3.1 4.1 + - - +
81A PRO* 3.3 19.1 - - + +
82A VAL* 2.9 27.4 + - - +
172A VAL* 3.9 5.6 - - - -
173A TYR* 5.1 0.2 - - + -
174A ALA* 3.5 15.0 - - + +
176A ALA* 4.7 4.3 - - + -
191A MET* 4.0 27.8 - - + -
194A LEU* 4.1 14.4 - - + -
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Residues in contact with ALA 32 (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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31A VAL* 1.3 73.2 - - - +
33A ILE* 1.3 58.5 + - - +
34A ASP 4.2 0.3 + - - -
82A VAL* 3.5 16.2 - - + +
84A VAL* 4.3 0.9 - - + -
163A CYS* 4.0 25.6 - - + -
166A LEU* 4.1 11.9 - - + -
172A VAL* 3.9 19.1 - - + +
174A ALA 2.9 8.9 + - - +
175A ALA* 3.4 3.6 - - - +
176A ALA 2.7 32.4 + - - +
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Residues in contact with ILE 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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31A VAL* 4.2 6.1 - - + -
32A ALA* 1.3 77.9 - - - +
34A ASP* 1.3 69.0 + - - +
35A ALA 3.1 2.6 + - - -
38A SER* 4.5 9.0 - - - +
74A MET* 3.8 28.0 - - + -
81A PRO* 3.6 30.7 - - + -
82A VAL 2.9 8.7 + - - +
83A TYR* 3.5 33.5 - - + -
84A VAL* 2.7 33.1 + - - +
163A CYS* 4.3 3.4 - - - -
176A ALA* 3.7 22.2 - - + +
194A LEU* 5.4 0.2 - - + -
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Residues in contact with ASP 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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32A ALA 4.2 0.4 + - - -
33A ILE* 1.3 76.6 - - - +
35A ALA* 1.3 65.5 + - - +
36A SER* 3.4 10.2 + - - -
37A MET* 3.3 32.2 + - + +
38A SER* 3.3 15.1 + - - -
84A VAL 3.9 3.4 - - - -
86A ASP* 4.4 1.4 - - - +
159A ALA* 4.2 14.9 - - - +
160A GLU* 4.0 25.1 + - - +
163A CYS* 4.3 12.7 - - - -
176A ALA 3.6 5.8 + - - +
177A THR* 4.2 21.8 + - + +
1001A SM 4.1 8.8 - - - -
1201A SO4 5.0 0.3 + - - -
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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