Contacts of the strand formed by residues 19 - 27 (chain C) in PDB entry 3QN3
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 PRO 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C GLU* 3.8 17.7 - - - +
12C VAL 3.1 12.3 - - - +
13C LEU* 4.4 1.7 - - + -
14C ASP* 4.7 1.2 - - - +
18C ASN* 1.3 94.4 - - + +
20C THR* 1.3 62.7 + - - +
52C ARG* 2.8 25.2 + - - -
58C PHE* 3.4 52.7 - - + -
61C LYS* 3.3 27.6 - - + +
62C GLY* 4.0 0.9 - - - -
63C VAL* 4.2 6.5 - - + -
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Residues in contact with THR 20 (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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11C GLU* 3.5 0.9 - - - -
12C VAL* 2.9 37.3 + - + +
14C ASP* 4.2 24.2 - - + +
19C PRO* 1.3 76.4 - - - +
21C VAL* 1.3 63.4 + - - +
36C ILE* 3.7 21.1 - - + -
37C VAL* 2.7 34.9 + - - +
38C PRO 4.2 6.0 + - - -
39C SER* 4.7 3.1 + - - -
50C GLU* 5.5 0.5 + - - -
52C ARG* 5.2 3.4 + - - +
63C VAL* 3.5 19.1 - - - +
108C ASN* 5.0 4.5 + - - +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 3.8 26.2 - - + -
10C TYR 3.9 3.4 - - - -
12C VAL* 4.4 2.0 - - - -
20C THR* 1.3 79.7 + - - +
22C LYS* 1.3 65.0 + - - +
23C ALA* 4.6 3.6 - - + +
36C ILE* 3.6 3.1 - - - +
37C VAL* 3.1 32.2 + - + +
63C VAL* 3.7 17.9 - - + -
66C ALA* 3.5 30.1 - - + -
67C VAL* 4.1 8.3 - - + -
70C VAL* 4.6 10.3 - - + -
108C ASN* 3.6 31.0 - - + +
109C ALA 5.5 0.2 - - - +
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Residues in contact with LYS 22 (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 ALA* 3.1 5.2 - - - +
10C TYR* 3.0 69.1 + - + +
12C VAL* 3.9 25.5 - - + +
20C THR 3.9 0.6 + - - -
21C VAL* 1.3 73.9 - - - +
23C ALA* 1.3 67.6 + - - +
34C ALA* 3.8 25.3 - - - +
35C ALA 3.3 11.0 - - - +
36C ILE* 3.7 27.2 - - + +
366C GLU* 5.5 1.4 + - - -
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Residues in contact with ALA 23 (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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7C VAL* 5.7 0.2 - - + -
8C ARG 3.3 8.5 - - - +
9C ALA* 4.5 6.3 - - + -
10C TYR* 5.4 0.7 - - - -
21C VAL* 4.1 3.8 - - + -
22C LYS* 1.3 77.7 - - - +
24C GLU* 1.3 62.1 + - - +
25C VAL* 5.6 0.4 - - + -
34C ALA* 3.1 5.5 - - - +
35C ALA 2.8 32.8 + - - -
70C VAL* 5.3 0.7 - - + -
112C GLY* 3.6 34.5 - - - +
113C VAL* 3.8 16.4 - - + +
116C ALA* 3.7 2.6 - - + +
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Residues in contact with GLU 24 (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 ASP* 4.0 3.5 - - - +
7C VAL* 3.5 2.9 - - - +
8C ARG* 2.8 72.6 + - + +
10C TYR* 4.4 18.4 + - + +
23C ALA* 1.3 75.3 - - - +
25C VAL* 1.3 62.9 + - - +
26C THR* 4.1 11.8 + - - -
32C VAL* 3.5 31.0 - - + +
33C GLY 3.3 5.6 - - - +
34C ALA* 4.6 8.5 - - + +
116C ALA* 4.3 0.2 - - - -
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Residues in contact with VAL 25 (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 ILE* 4.0 18.6 - - + -
6C ASP 3.2 8.7 - - - +
7C VAL* 4.2 18.6 - - + -
24C GLU* 1.3 80.7 - - - +
26C THR* 1.3 62.6 + - - +
27C LEU* 4.1 17.5 - - + -
32C VAL* 3.3 4.0 - - - -
33C GLY 2.8 34.3 + - - +
113C VAL* 4.2 6.7 - - + +
116C ALA* 3.6 24.7 - - + +
117C THR* 3.6 29.4 - - - +
120C ALA* 3.6 3.7 - - + +
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Residues in contact with THR 26 (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 ILE* 3.8 2.6 - - - -
5C GLU* 2.7 37.3 + - + +
6C ASP* 2.8 37.5 + - + +
24C GLU* 4.1 12.7 + - - +
25C VAL* 1.3 75.1 - - - +
27C LEU* 1.3 69.0 + - - +
30C GLY* 4.2 14.1 - - - +
31C SER 3.3 8.5 - - - +
32C VAL* 3.7 15.1 - - + +
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Residues in contact with LEU 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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2C LEU* 3.9 20.0 - - + -
3C VAL 3.4 9.4 - - - +
4C ILE* 4.1 11.4 - - + -
5C GLU* 3.9 6.2 - - - +
25C VAL* 4.1 8.3 - - + -
26C THR* 1.3 86.6 - - - +
28C SER* 1.3 59.3 + - - +
29C ASP* 3.2 14.1 - - - +
30C GLY* 2.8 21.9 + - - -
31C SER* 2.8 10.8 + - - +
83C ALA* 3.7 31.2 - - + -
117C THR* 5.0 3.8 - - + -
120C ALA* 3.4 46.2 - - + +
121C ALA* 3.7 7.0 - - - +
124C ALA* 4.0 2.5 - - + -
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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