Contacts of the helix formed by residues 10 - 19 (chain C) in PDB entry 2QC8
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 ASN 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 5.6 3.0 + - - -
11C LYS* 1.3 74.9 + - - +
12C GLY* 3.6 14.4 + - - +
13C ILE* 3.2 35.5 + - + +
14C LYS 3.3 8.0 + - - -
10D ASN* 5.7 3.5 + - - -
11D LYS* 5.8 1.7 - - - +
174D ASP* 4.4 7.8 + - - -
232D PHE* 3.5 30.7 + - - +
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Residues in contact with LYS 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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10B ASN* 5.7 2.7 - - - +
13B ILE* 3.6 36.3 - - + +
10C ASN* 1.3 80.5 - - - +
12C GLY* 1.3 65.8 + - - +
14C LYS* 3.2 12.5 + - + +
15C GLN* 3.1 23.0 + - - +
230C GLU* 4.2 5.9 + - - +
231C ASP* 3.3 41.3 + - + +
174D ASP* 2.9 41.1 + - - +
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Residues in contact with GLY 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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10C ASN* 3.4 11.7 + - - +
11C LYS* 1.3 75.7 - - - +
13C ILE* 1.3 65.0 + - - +
15C GLN* 3.4 12.9 + - - +
16C VAL* 3.6 17.7 + - - +
11D LYS* 5.9 1.8 - - - -
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Residues in contact with ILE 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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10C ASN* 3.2 33.4 + - + +
12C GLY* 1.3 71.9 - - - +
14C LYS* 1.3 67.8 + - - +
16C VAL* 3.1 17.8 + - + +
17C TYR* 3.4 18.7 - - + -
11D LYS* 3.6 31.6 - - + +
231D ASP* 3.0 45.3 - - + +
232D PHE* 3.5 35.0 - - + -
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Residues in contact with LYS 14 (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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10C ASN 3.3 5.8 + - - +
11C LYS* 3.2 16.7 + - + +
13C ILE* 1.3 80.8 - - - +
15C GLN* 1.3 67.9 + - - +
17C TYR* 3.0 8.6 + - - +
18C MET* 3.0 43.0 + - + +
89C PHE* 5.3 5.1 + - - +
227C ARG* 4.1 21.2 - - - +
231C ASP* 4.2 15.2 + - - -
174D ASP* 3.5 38.6 + - + +
177D GLU* 4.1 19.2 - - + +
178D ALA* 5.0 2.2 - - + -
232D PHE* 4.0 17.0 - - + -
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Residues in contact with GLN 15 (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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16B VAL* 3.4 45.3 - - + +
11C LYS 3.1 15.3 + - - +
12C GLY* 3.8 8.5 - - - +
13C ILE 3.2 0.4 - - - -
14C LYS* 1.3 81.5 - - - +
16C VAL* 1.3 54.4 + - + +
18C MET* 3.3 19.3 + - - +
19C SER* 2.8 40.9 + - - +
91C LYS* 6.3 0.8 - - - +
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Residues in contact with VAL 16 (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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12C GLY 3.6 14.3 + - - +
13C ILE* 3.1 9.6 + - - +
14C LYS 3.1 0.6 + - - -
15C GLN* 1.3 74.1 - - + +
17C TYR* 1.3 71.0 + - + +
19C SER* 3.3 19.6 + - - -
20C LEU* 3.8 8.4 + - + +
11D LYS 6.1 0.2 - - - +
15D GLN* 3.6 46.9 - - + +
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Residues in contact with TYR 17 (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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13C ILE* 3.4 29.2 - - + -
14C LYS 3.0 6.0 + - - +
16C VAL* 1.3 82.5 - - + +
18C MET* 1.3 57.6 + - - +
20C LEU* 3.1 32.2 + - + +
88D PRO 4.6 4.5 - - - -
89D PHE* 3.3 40.0 - + - -
178D ALA* 3.6 46.2 - - + +
181D ARG* 3.3 17.0 - - + +
182D ALA* 4.0 10.8 - - + -
228D VAL* 3.8 17.5 - - + -
231D ASP* 2.4 32.1 + - - -
232D PHE* 4.4 3.4 - + - -
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Residues in contact with MET 18 (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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14C LYS* 3.0 48.1 + - + +
15C GLN* 3.7 23.1 + - - +
16C VAL 3.2 0.6 - - - -
17C TYR* 1.3 78.5 - - + +
19C SER* 1.3 55.7 + - - +
20C LEU 3.4 0.4 - - - -
27C GLN* 5.8 0.2 - - - +
89C PHE 3.7 23.6 - - - +
90C ARG* 4.1 13.2 - - + +
91C LYS* 6.1 1.2 - - - +
177D GLU* 4.1 28.7 - - - +
178D ALA 4.9 0.7 - - - -
181D ARG* 3.0 55.6 + - - +
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Residues in contact with SER 19 (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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15C GLN* 2.8 27.2 + - - +
16C VAL* 3.5 12.0 + - - -
17C TYR 3.2 0.2 - - - -
18C MET* 1.3 75.8 - - - +
20C LEU* 1.3 64.0 + - - +
21C PRO* 3.3 8.8 - - - +
91D LYS* 5.2 6.1 + - - -
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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