Contacts of the strand formed by residues 26 - 35 (chain C) in PDB entry 1QA7
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 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLY* 3.0 20.2 - - - -
18C VAL* 2.8 27.8 + - + +
24C SER* 3.8 2.3 + - - +
25C VAL* 1.3 70.6 - - - +
27C TRP* 1.3 64.5 + - - +
28C VAL* 3.3 15.8 + - + +
49C GLU* 4.5 17.2 + - - -
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Residues in contact with TRP 27 (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* 3.8 27.8 - - + -
16C PHE 3.6 3.8 - - - -
17C GLY* 3.7 20.9 - - - -
25C VAL* 3.6 28.1 + - + +
26C ARG* 1.3 73.6 - - - +
28C VAL* 1.3 59.0 + - - +
58C TYR* 4.0 16.2 - - + -
60C ASN* 3.8 14.1 - - + -
65C TYR* 3.6 59.9 + + + -
301C IVF 3.2 29.5 - - + +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 2.7 20.3 + - + +
17C GLY* 4.6 1.8 - - - -
18C VAL* 4.6 10.5 - - + +
26C ARG* 3.6 25.4 - - + +
27C TRP* 1.3 71.5 - - - +
29C MET* 1.3 56.5 + - + +
44C HIS 5.1 0.9 - - - +
45C ALA* 3.6 37.9 - - + +
49C GLU* 4.7 5.8 - - - +
147C LYS* 6.2 0.2 - - - +
301C IVF 2.8 62.7 + - + +
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Residues in contact with MET 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 2.7 32.6 + - + -
28C VAL* 1.3 77.0 - - - +
30C ASN* 1.3 61.3 + - - +
42C PRO* 3.5 32.3 - - - -
44C HIS* 4.2 15.9 - - + +
45C ALA* 3.5 44.4 - - + +
170C GLY 4.9 0.4 - - - -
172C CYS* 3.4 32.8 - - + +
301C IVF 3.1 44.3 - - + +
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Residues in contact with ASN 30 (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 LEU* 4.3 10.9 - - + +
14C VAL 3.3 14.6 - - - +
15C GLN* 4.2 6.6 - - - +
16C PHE* 4.2 4.3 - - - +
29C MET* 1.3 92.9 - - - +
31C ALA* 1.3 63.3 + - - +
42C PRO* 4.0 5.7 - - - +
121C THR* 2.8 22.3 - - + +
122C THR* 3.0 27.5 + - - +
170C GLY 2.8 29.1 + - - -
172C CYS 3.0 7.3 + - - +
173C GLY* 3.6 20.4 - - - +
301C IVF 3.9 7.9 - - - -
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Residues in contact with ALA 31 (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 ASN 4.0 0.5 - - - +
13C LEU* 3.5 9.0 - - - +
14C VAL* 2.9 44.9 + - + +
16C PHE* 4.5 7.4 - - + -
30C ASN* 1.3 75.9 - - - +
32C LEU* 1.3 61.9 + - - +
33C GLY 4.1 0.2 - - - -
39C LEU* 4.7 6.5 - - + -
40C LEU 3.5 13.5 - - - +
41C VAL* 4.0 21.3 - - + +
59C PHE* 4.9 4.9 - - + -
173C GLY* 4.4 4.0 - - - -
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Residues in contact with LEU 32 (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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9C VAL* 3.7 20.6 - - + +
12C ASN* 3.7 26.5 - - + +
13C LEU* 3.7 13.2 - - + -
31C ALA* 1.3 74.7 - - - +
33C GLY* 1.3 69.3 + - - +
34C VAL* 3.5 3.2 + - + +
39C LEU* 3.2 3.3 - - - -
40C LEU* 2.6 43.2 + - + +
99C ILE* 4.4 7.9 - - + -
103C PHE* 4.2 19.3 - - + -
173C GLY 4.4 1.9 + - - +
175C ALA* 3.6 29.8 - - + -
187C ILE* 5.1 0.2 - - + -
190C ILE* 4.0 23.3 - - + -
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Residues in contact with GLY 33 (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 ASN* 2.5 45.1 + - - +
31C ALA 4.0 0.4 + - - -
32C LEU* 1.3 73.4 - - - +
34C VAL* 1.3 56.2 + - - -
35C LYS 3.8 0.7 - - - -
38C TRP 3.6 9.4 - - - -
39C LEU* 3.9 1.3 - - - -
96C PHE* 3.5 30.9 - - - -
99C ILE* 3.4 8.1 - - - +
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Residues in contact with VAL 34 (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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32C LEU* 4.0 2.5 - - + +
33C GLY* 1.3 73.7 - - - +
35C LYS* 1.3 63.8 + - + +
38C TRP* 3.1 32.3 + - + +
39C LEU* 4.1 7.0 - - - +
40C LEU* 3.6 26.9 - - + -
87C LEU* 5.0 3.8 - - + -
97C ARG 4.1 1.8 - - - -
99C ILE* 2.8 35.0 + - + +
100C THR* 3.1 7.4 - - + +
103C PHE* 4.0 9.6 - - + -
209C PHE* 3.0 45.8 - - + -
212C ILE* 5.1 0.4 - - + -
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Residues in contact with LYS 35 (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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33C GLY 3.8 0.6 - - - -
34C VAL* 1.3 84.4 - - + +
36C ASP* 1.3 98.5 + - + +
37C ASP 3.1 0.2 + - - -
38C TRP* 2.9 25.1 + - + +
96C PHE* 3.9 12.7 - - - +
97C ARG 4.0 2.7 - - - -
98C ASP* 3.5 30.3 - - + +
100C THR* 3.4 26.2 + - + +
209C PHE* 4.2 6.9 - - - +
212C ILE* 4.5 7.9 - - + +
213C ASP* 4.1 31.6 - - - +
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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