Contacts of the strand formed by residues 9 - 18 (chain C) in PDB entry 3UYT
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 TYR 9 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ARG* 3.2 10.0 - - - +
5C VAL* 2.7 44.0 + - + +
6C GLY* 4.2 10.3 - - - -
7C ASN 3.5 0.2 - - - -
8C ARG* 1.3 109.5 + - + +
10C ARG* 1.3 60.7 + - - +
27C THR 3.3 3.4 - - - +
28C ASP* 3.6 35.5 + - + -
29C ILE* 5.2 1.8 - - - -
35C VAL* 4.2 12.3 - - + -
37C ILE* 4.4 14.8 - - + -
69C ARG* 3.8 16.5 + - + +
70C TRP* 3.5 40.5 - + + +
81C VAL* 4.1 25.6 - - + -
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Residues in contact with ARG 10 (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 ARG* 4.5 11.0 - - + -
9C TYR* 1.3 74.2 - - - +
11C LEU* 1.3 65.3 + - - +
12C GLY* 3.5 1.7 + - - +
26C GLY* 3.1 26.2 - - - -
27C THR* 3.0 25.3 + - - +
29C ILE* 3.8 29.3 - - + +
37C ILE* 3.9 3.9 - - - +
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Residues in contact with LEU 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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4C ARG* 4.7 6.5 - - - +
5C VAL* 3.6 29.5 - - + +
9C TYR 4.1 1.4 + - - -
10C ARG* 1.3 75.4 - - - +
12C GLY* 1.3 69.5 + - - +
24C TYR* 3.8 33.2 - - + -
25C LEU 4.3 1.1 - - - -
37C ILE* 3.9 22.9 - - + -
39C LEU* 3.8 27.6 - - + -
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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 ARG* 3.5 5.3 + - - +
11C LEU* 1.3 81.2 - - - +
13C ARG* 1.3 65.3 + - - +
24C TYR* 3.6 12.3 - - - -
25C LEU* 2.8 22.4 + - - -
26C GLY* 4.9 0.9 - - - -
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Residues in contact with ARG 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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12C GLY* 1.3 75.2 - - - -
14C LYS* 1.3 72.1 + - - +
15C ILE* 3.4 5.2 + - + +
24C TYR* 3.4 3.8 - - - -
25C LEU* 3.0 27.4 + - + +
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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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13C ARG* 1.3 82.3 - - - +
15C ILE* 1.3 62.0 + - - +
16C GLY* 3.6 22.2 - - - +
17C SER* 4.4 5.4 + - - -
22C ASP* 3.0 41.0 + - + +
23C ILE 3.5 4.5 - - - +
24C TYR* 3.4 30.6 - - + +
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Residues in contact with ILE 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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13C ARG* 3.4 10.7 + - + +
14C LYS* 1.3 77.9 - - - +
16C GLY* 1.3 57.4 + - - +
23C ILE* 2.8 40.6 + - + +
24C TYR 4.0 2.2 - - - +
25C LEU* 3.8 43.7 - - + +
36C ALA* 5.4 0.9 - - + -
84C LEU* 5.3 0.2 - - + -
295C 0CK 3.9 36.2 - - + +
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Residues in contact with GLY 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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14C LYS* 3.6 18.8 - - - +
15C ILE* 1.3 82.7 - - - +
17C SER* 1.3 67.5 + - - -
22C ASP* 3.7 2.4 - - - +
23C ILE* 2.9 26.1 + - - +
295C 0CK 4.9 6.7 - - - -
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Residues in contact with SER 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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14C LYS* 4.4 5.9 + - - -
16C GLY* 1.3 78.3 - - - -
18C GLY* 1.3 64.2 + - - +
21C GLY 3.4 9.4 - - - -
22C ASP* 3.4 17.6 + - - -
23C ILE* 4.0 9.1 - - - +
295C 0CK 4.2 13.2 - - - +
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Residues in contact with GLY 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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17C SER* 1.3 81.2 - - - +
19C SER* 1.3 67.1 + - - -
20C PHE 3.3 2.4 + - - -
21C GLY 2.9 15.0 + - - +
23C ILE* 3.7 2.8 - - - +
38C LYS* 4.3 6.5 - - - -
149C ASP* 3.7 10.8 - - - -
295C 0CK 4.3 10.8 - - - -
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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