Contacts of the helix formed by residues 5 - 13 (chain C) in PDB entry 4XQ2
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 ARG 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B ASP* 3.3 37.5 + - - +
367B GLN* 4.0 14.5 - - - +
368B ASP* 2.6 38.7 + - - +
371B GLU* 3.7 28.7 + - - -
4C MSE 1.3 75.6 - - - +
6C PHE* 1.3 67.7 + - - +
7C GLY 3.2 0.4 - - - -
8C THR* 2.8 13.3 + - - -
9C ARG* 3.1 18.1 + - - +
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Residues in contact with PHE 6 (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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5C ARG* 1.3 71.3 - - - +
7C GLY* 1.3 59.4 + - - +
8C THR 2.8 6.4 + - - -
9C ARG* 3.1 38.2 + - - +
10C LEU* 3.3 35.3 + - + +
64C LEU* 3.5 55.0 - - + -
178C PRO* 3.3 35.4 - - + -
179C VAL* 3.8 23.3 - - + -
182C GLN* 4.5 3.1 - - - -
247C LEU* 4.7 0.4 - - + -
248C SER* 4.7 5.6 - - - -
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Residues in contact with GLY 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ILE 3.3 7.4 - - - +
364B GLU* 3.1 11.1 - - - -
365B ASP* 3.0 29.5 + - - -
5C ARG* 3.1 4.6 + - - +
6C PHE* 1.3 80.8 - - - +
8C THR* 1.3 54.3 + - - +
10C LEU* 4.5 13.8 - - - +
11C VAL* 4.5 3.5 - - - +
248C SER* 5.1 6.7 - - - -
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Residues in contact with THR 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 4.0 25.4 - - + -
364B GLU* 3.4 7.7 - - + +
365B ASP 2.8 20.5 + - - +
368B ASP* 2.7 25.9 + - - +
4C MSE 3.7 27.4 - - + -
5C ARG 2.8 9.3 + - - -
7C GLY* 1.3 73.6 - - - +
9C ARG* 1.3 62.3 + - - +
10C LEU 3.1 2.2 - - - -
11C VAL* 2.9 21.0 + - - +
12C HIS* 3.0 15.7 + - + +
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Residues in contact with ARG 9 (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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4C MSE 3.2 49.3 + - + +
5C ARG* 3.1 9.6 + - - +
6C PHE* 3.1 43.6 + - - +
8C THR* 1.3 72.9 - - - +
10C LEU* 1.3 61.7 + - - +
13C GLY* 2.8 33.9 + - - +
60C CYS* 3.8 6.7 - - - +
63C GLY* 3.4 29.2 + - - +
64C LEU* 4.0 16.7 + - + +
66C ARG* 3.7 38.4 - - - +
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Residues in contact with LEU 10 (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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6C PHE* 3.6 27.1 - - + +
7C GLY* 4.5 6.7 - - - +
8C THR 3.1 0.4 - - - -
9C ARG* 1.3 78.9 - - - +
11C VAL* 1.3 60.8 + - + +
60C CYS* 4.6 2.2 - - - -
64C LEU* 3.5 25.4 - - + -
241C ARG* 2.9 31.9 + - - +
244C LEU* 3.5 37.9 - - + +
245C HIS* 3.5 17.6 + - - +
247C LEU* 4.4 2.5 - - + -
248C SER* 3.5 42.8 - - - +
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Residues in contact with VAL 11 (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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327B VAL 3.9 13.5 - - - +
328B HIS* 3.6 22.9 - - + -
363B ILE* 3.9 27.8 - - + +
364B GLU* 3.7 20.9 - - + +
7C GLY 4.5 4.5 - - - +
8C THR 2.9 7.9 + - - +
10C LEU* 1.3 81.5 - - + +
12C HIS* 1.3 78.6 - - + +
15C ARG* 4.0 9.5 - - - -
241C ARG* 3.2 7.5 + - - -
245C HIS* 2.9 31.7 - - + +
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Residues in contact with HIS 12 (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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317B LEU* 3.6 32.6 - - + +
319B THR* 4.8 1.6 - - - -
328B HIS* 4.3 9.4 - - + -
329B SER 5.3 0.4 - - - -
364B GLU* 2.8 37.4 + - + +
4C MSE 4.5 19.0 - - - +
8C THR* 3.0 11.5 + - + +
9C ARG* 5.0 0.2 - - - -
11C VAL* 1.3 94.5 - - + +
13C GLY* 1.3 67.0 + - - +
14C GLY 3.3 0.7 + - - -
15C ARG* 3.1 59.9 + - + +
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Residues in contact with GLY 13 (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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4C MSE 5.2 6.5 - - - +
9C ARG* 2.8 31.4 + - - +
12C HIS* 1.3 70.2 - - - +
14C GLY* 1.3 61.9 + - - -
59C GLU 5.1 1.6 - - - -
60C CYS* 3.4 17.6 - - - +
63C GLY* 6.3 1.3 - - - -
241C ARG* 2.7 30.8 + - - -
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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