Contacts of the helix formed by residues 7 - 20 (chain A) in PDB entry 6D6Q
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 SER 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO 3.9 2.6 + - - -
6A LEU* 1.3 78.0 - - - +
8A ASN* 1.3 65.5 + - - +
9A CYS* 3.8 9.0 + - - +
10A GLU* 3.3 31.7 + - - +
11A ARG* 3.2 20.1 + - - +
120G ILE* 4.3 25.7 - - - +
160G GLY 3.8 13.7 - - - -
162G LEU* 5.1 7.2 - - - -
199G LEU* 4.6 6.8 - - - +
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Residues in contact with ASN 8 (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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6A LEU 4.9 1.7 - - - +
7A SER* 1.3 71.5 - - - +
9A CYS* 1.3 66.3 + - - +
11A ARG* 3.6 24.0 + - - +
12A ARG* 2.9 38.1 + - + +
158G GLN* 5.7 2.2 - - - +
159G VAL 3.4 24.0 + - - -
160G GLY* 3.5 19.1 + - - +
161G ASP* 4.1 2.7 - - - +
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Residues in contact with CYS 9 (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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7A SER* 3.1 8.2 - - - +
8A ASN* 1.3 77.9 - - - +
10A GLU* 1.3 65.1 + - + +
12A ARG* 3.9 5.0 - - - +
13A PHE* 2.9 25.3 + - - +
160G GLY 5.2 0.2 + - - -
162G LEU* 4.2 22.7 - - + +
194G GLY 5.5 0.2 - - - +
195G GLN* 5.1 7.2 - - - +
196G ASP 4.8 5.8 + - - +
197G GLY 2.8 47.0 + - - +
198G LEU* 4.1 2.9 - - - -
199G LEU* 4.5 3.1 - - + -
238G TRP* 3.6 22.0 - - - -
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Residues in contact with GLU 10 (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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6A LEU* 3.0 27.6 - - + +
7A SER* 3.3 21.7 + - - +
9A CYS* 1.3 79.7 - - - +
11A ARG* 1.3 62.7 + - - +
13A PHE* 3.4 5.5 + - - +
14A LEU* 2.9 36.7 + - + +
212A ARG* 3.7 28.6 + - - +
197G GLY 5.1 0.7 - - - -
198G LEU* 5.1 4.7 - - + -
199G LEU* 2.5 54.1 - - + +
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Residues in contact with ARG 11 (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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6A LEU* 4.0 34.1 + - + +
7A SER 3.2 10.5 + - - +
8A ASN* 3.6 25.6 + - - +
10A GLU* 1.3 79.4 - - - +
12A ARG* 1.3 65.6 + - + +
14A LEU* 3.2 2.3 + - - +
15A LEU* 3.0 43.7 + - + +
215A ARG 5.2 4.4 + - - -
216A VAL* 3.9 27.1 - - + +
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Residues in contact with ARG 12 (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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8A ASN* 2.9 28.7 + - + +
9A CYS* 4.0 4.5 - - - +
11A ARG* 1.3 78.4 - - + +
13A PHE* 1.3 64.1 + - - +
15A LEU* 3.3 10.5 + - + +
16A ARG* 2.9 47.6 + - + +
195G GLN* 2.5 50.2 + - - +
196G ASP* 5.4 9.3 - - - +
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Residues in contact with PHE 13 (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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9A CYS 2.9 18.1 + - - +
10A GLU* 3.7 4.9 - - - +
12A ARG* 1.3 76.7 - - - +
14A LEU* 1.3 63.0 + - + +
16A ARG* 3.7 9.0 - - - +
17A ALA* 2.9 32.0 + - + +
24A LEU* 3.9 9.4 - - + -
196G ASP* 5.5 3.8 - - - -
197G GLY* 3.6 25.6 - - - +
198G LEU* 3.7 22.7 - - + -
244G ILE* 3.6 37.7 - - + -
247G THR* 3.9 25.1 - - + -
248G LEU* 3.2 36.8 - - + -
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Residues in contact with LEU 14 (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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6A LEU* 5.6 1.6 - - + -
10A GLU* 2.9 32.8 + - + +
11A ARG 3.6 3.6 - - - +
13A PHE* 1.3 77.8 - - + +
15A LEU* 1.3 66.9 + - - +
17A ALA* 3.2 4.6 + - - +
18A ILE* 2.9 33.1 + - + +
24A LEU* 3.5 40.4 - - + -
212A ARG* 4.0 35.0 - - + +
213A GLU* 4.8 8.5 - - + +
216A VAL* 3.9 33.4 - - + -
198G LEU* 5.9 1.3 - - + -
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Residues in contact with LEU 15 (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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11A ARG* 3.0 39.3 + - + +
12A ARG* 3.8 8.5 - - + +
14A LEU* 1.3 76.7 - - + +
16A ARG* 1.3 58.3 + - + +
18A ILE* 3.3 7.8 + - + +
19A GLU* 2.9 32.5 + - - +
199A PHE* 4.6 14.1 - - + -
200A GLN* 4.8 25.3 + - + +
216A VAL* 4.4 23.1 - - + +
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Residues in contact with ARG 16 (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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12A ARG* 2.9 40.2 + - + +
13A PHE* 3.7 8.2 - - - +
15A LEU* 1.3 76.1 - - + +
17A ALA* 1.3 59.3 + - - +
19A GLU* 3.1 11.7 + - + +
20A GLU* 2.9 38.4 + - - +
196G ASP* 2.7 40.8 + - - +
242G LYS 5.9 0.4 + - - -
244G ILE* 4.0 30.0 - - + +
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Residues in contact with ALA 17 (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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13A PHE* 2.9 26.6 + - + +
14A LEU* 3.8 6.3 - - - +
16A ARG* 1.3 76.4 - - - +
18A ILE* 1.3 53.5 + - + +
20A GLU* 3.4 6.1 - - - +
21A LYS 2.9 6.9 + - - -
22A LYS* 2.6 57.1 + - + +
24A LEU* 5.1 4.9 - - + -
244G ILE* 4.4 19.0 - - + +
248G LEU* 5.0 2.5 - - + -
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Residues in contact with ILE 18 (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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14A LEU* 2.9 25.7 + - + +
15A LEU* 3.5 10.1 - - + +
17A ALA* 1.3 74.8 - - + +
19A GLU* 1.3 59.6 + - - +
20A GLU 3.0 1.8 - - - -
21A LYS* 2.6 30.4 + - - +
22A LYS 4.4 9.9 - - - +
23A ARG* 4.5 6.1 - - - -
24A LEU* 6.0 3.1 - - + -
29A THR* 6.2 1.1 - - + -
199A PHE* 4.5 20.0 - - + -
204A TYR* 3.7 37.7 - - + -
206A LEU* 3.7 39.3 - - + -
213A GLU* 5.1 5.2 - - + +
216A VAL* 6.6 0.2 - - + -
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Residues in contact with GLU 19 (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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15A LEU 2.9 22.0 + - - +
16A ARG* 3.3 12.8 - - + +
18A ILE* 1.3 77.3 - - - +
20A GLU* 1.3 61.9 + - + +
21A LYS* 3.6 4.7 + - - +
200A GLN* 2.4 44.4 + - - +
204A TYR* 2.7 43.0 + - - -
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Residues in contact with GLU 20 (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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16A ARG* 2.9 20.7 + - - +
17A ALA* 3.4 4.0 - - - +
19A GLU* 1.3 78.1 - - + +
21A LYS* 1.3 71.4 + - - +
22A LYS* 3.2 28.5 + - + +
243G THR* 5.4 1.7 + - - -
244G ILE* 3.5 38.4 - - - +
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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