Contacts of the helix formed by residues 3 - 15 (chain X) in PDB entry 2QVY
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 THR 3 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1X MET* 3.5 27.8 - - + -
2X GLN* 1.3 76.2 - - - +
4X VAL* 1.3 54.6 + - - +
5X ASN* 3.6 6.7 + - - +
6X GLU* 2.9 30.5 + - + +
7X MET* 2.7 36.5 + - - +
75X HIS* 4.6 0.7 - - - -
150X ARG* 4.0 18.9 + - + -
175X GLN* 3.7 30.1 - - + +
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Residues in contact with VAL 4 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X THR* 1.3 68.9 - - - +
5X ASN* 1.3 69.9 + - - +
7X MET* 2.9 24.1 + - + +
8X LEU* 3.0 27.6 + - + +
72X LEU* 4.6 6.1 - - + -
75X HIS* 3.4 20.5 + - + +
157X PHE* 3.5 30.3 - - + -
175X GLN* 5.2 1.0 + - - +
178X ALA* 3.6 23.4 - - + +
211X PHE* 4.6 1.1 - - + -
212X PHE* 3.9 12.6 - - + -
216X VAL* 4.2 22.4 - - + -
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Residues in contact with ASN 5 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X THR* 3.3 5.5 + - - +
4X VAL* 1.3 74.9 - - - +
6X GLU* 1.3 66.7 + - - +
8X LEU* 3.2 5.3 + - - +
9X ARG* 2.9 33.0 + - - +
36X ARG* 3.3 30.5 + - - +
75X HIS* 2.9 28.1 + - + +
76X ARG* 3.8 15.4 - - - +
147X ASP* 3.0 33.1 + - - -
150X ARG* 4.0 18.5 - - - +
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Residues in contact with GLU 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X GLN* 4.2 5.2 - - + -
3X THR* 2.9 30.8 + - + +
5X ASN* 1.3 79.8 + - - +
7X MET* 1.3 68.5 + - - +
9X ARG* 2.6 44.1 + - - -
10X ARG* 2.6 70.9 + - - +
147X ASP* 5.0 2.8 - - - +
150X ARG* 6.4 0.2 - - - +
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Residues in contact with MET 7 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X GLN* 3.5 33.4 - - + +
3X THR 2.7 22.4 + - - +
4X VAL* 2.9 11.2 + - - +
6X GLU* 1.3 76.2 - - - +
8X LEU* 1.3 65.1 + - + +
10X ARG* 4.0 2.3 - - - +
11X ALA* 3.2 21.0 + - - +
14X ARG* 4.6 2.6 + - - -
178X ALA* 3.6 39.3 - - + -
179X GLU* 4.2 11.0 - - - +
182X VAL* 4.0 25.1 - - + -
183X LEU* 6.2 0.9 - - - -
216X VAL* 4.2 5.2 - - + -
220X ALA* 3.8 29.1 - - + +
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Residues in contact with LEU 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X VAL* 3.0 25.6 + - + +
5X ASN* 3.8 3.8 - - - +
7X MET* 1.3 76.5 - - - +
9X ARG* 1.3 59.9 + - - +
11X ALA* 3.4 5.4 - - - +
12X ALA* 3.0 25.5 + - - +
32X HIS* 4.8 2.8 + - - -
35X LEU* 5.8 1.6 - - + -
36X ARG* 4.2 22.0 + - - +
72X LEU* 3.6 41.7 - - + -
216X VAL* 4.1 18.8 - - + +
219X LEU* 3.5 38.4 - - + -
220X ALA* 3.9 10.3 - - + +
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Residues in contact with ARG 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ASN* 2.9 21.7 + - - +
6X GLU* 2.6 43.9 + - - +
8X LEU* 1.3 75.2 - - - +
10X ARG* 1.3 78.5 + - - +
12X ALA* 3.1 13.4 + - + +
13X THR* 3.0 36.1 - - + +
36X ARG* 4.1 24.6 - - - +
147X ASP* 5.0 10.0 + - - -
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Residues in contact with ARG 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET 4.5 9.7 + - - -
2X GLN* 2.8 48.2 + - - +
6X GLU* 2.6 48.7 + - - +
7X MET 4.0 2.2 - - - +
9X ARG* 1.3 85.8 - - - +
11X ALA* 1.3 62.8 + - - +
13X THR* 2.7 29.2 + - - -
14X ARG* 3.0 31.1 + - - +
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Residues in contact with ALA 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X MET 3.2 11.9 + - - +
8X LEU* 3.4 13.5 - - - +
10X ARG* 1.3 73.4 - - - +
12X ALA* 1.3 56.7 + - - +
14X ARG* 2.6 32.9 + - - +
15X ALA* 2.9 13.2 + - - +
32X HIS* 4.0 11.2 - - + +
219X LEU 3.7 18.8 - - - +
220X ALA* 4.4 1.1 - - - -
222X ASP* 3.2 25.4 - - - +
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Residues in contact with ALA 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X LEU 3.0 6.5 + - - +
9X ARG* 3.1 14.4 - - + +
11X ALA* 1.3 76.5 - - - +
13X THR* 1.3 56.9 + - + +
16X PRO* 3.1 34.3 - - - +
32X HIS* 4.0 21.1 + - + +
33X ALA* 5.3 2.0 - - - +
36X ARG* 3.5 34.3 - - + -
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Residues in contact with THR 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ARG* 3.0 37.2 - - + +
10X ARG* 2.7 16.7 + - - +
11X ALA 2.9 1.8 + - - -
12X ALA* 1.3 74.2 - - + +
14X ARG* 1.3 65.4 + - - +
16X PRO* 4.1 7.6 - - - +
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Residues in contact with ARG 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X GLN* 5.5 2.0 + - - -
7X MET 4.6 2.2 + - - -
10X ARG* 3.3 31.1 - - - +
11X ALA* 2.6 25.5 + - - +
13X THR* 1.3 78.2 - - - +
15X ALA* 1.3 49.7 + - - +
16X PRO* 3.6 4.4 - - - +
193X HIS* 3.9 15.4 + - - -
195X ARG* 2.7 25.6 + - - -
220X ALA 3.3 19.4 + - - -
222X ASP* 2.7 40.2 + - - +
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Residues in contact with ALA 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X ALA 2.9 9.2 + - - +
12X ALA 3.6 2.0 - - - -
14X ARG* 1.3 81.2 - - - +
16X PRO* 1.3 69.2 - - - +
17X ASP 3.2 2.2 - - - -
18X HIS* 3.0 21.0 + - + +
32X HIS* 3.4 18.3 - - + +
195X ARG* 3.4 28.7 - - - +
222X ASP* 4.4 17.0 - - + -
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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