Contacts of the strand formed by residues 32 - 39 (chain C) in PDB entry 2DFD
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 VAL 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ASN* 4.7 0.7 - - - -
7C ALA* 3.5 5.8 - - + +
9C VAL* 4.3 21.5 - - + -
26C LEU* 3.5 40.8 - - + +
29C SER* 3.2 16.8 + - - +
30C PRO* 3.2 4.0 - - - +
31C LEU* 1.3 81.8 - - + +
33C SER* 1.3 57.9 + - - +
34C ARG 3.5 27.8 - - - +
35C LEU* 4.3 9.9 - - + -
56C LYS* 4.9 3.1 - - - +
57C ALA* 3.3 26.3 + - + +
241C VAL* 5.5 1.3 - - + -
242C PHE* 4.5 4.5 - - + -
245C VAL* 6.1 1.1 - - + -
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Residues in contact with SER 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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6C ASN* 3.2 37.8 + - - -
7C ALA 2.8 11.6 + - - +
8C LYS* 4.1 9.4 + - - +
32C VAL* 1.3 74.1 - - - +
34C ARG* 1.3 63.0 + - - +
56C LYS* 4.2 5.3 - - - +
57C ALA* 3.4 7.5 - - - +
58C ALA* 3.1 20.6 + - - +
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Residues in contact with ARG 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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7C ALA 3.4 1.2 + - - -
8C LYS* 3.6 36.2 - - + +
9C VAL 3.0 26.6 + - - +
32C VAL* 3.5 9.0 - - - +
33C SER* 1.3 82.1 + - - +
35C LEU* 1.3 63.2 + - - +
36C THR* 3.6 24.5 + - + +
58C ALA* 3.5 19.1 - - + +
60C LYS* 5.7 4.5 - - + -
70C ASP 5.9 1.1 + - - -
71C CYS 4.5 2.2 + - - -
73C LYS 2.9 28.8 + - - -
74C GLY* 3.5 12.5 - - - -
75C CYS* 3.5 23.8 - - - -
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Residues in contact with LEU 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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9C VAL* 3.3 13.7 - - + +
11C VAL* 4.0 5.4 - - + -
23C SER* 3.3 29.2 - - - +
26C LEU* 3.9 30.1 - - + -
27C LYS* 3.8 22.0 - - + +
32C VAL* 4.3 7.9 - - + -
34C ARG* 1.3 72.5 - - - +
36C THR* 1.3 61.5 + - - +
37C LEU* 3.7 26.7 - - + -
50C LEU* 4.5 4.3 - - + -
57C ALA* 4.6 4.0 - - + +
58C ALA 2.8 12.3 + - - +
59C VAL* 3.3 18.2 - - + +
60C LYS 3.0 24.6 + - - +
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Residues in contact with THR 36 (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 2.9 7.9 + - - +
10C ALA* 3.1 15.4 - - - +
11C VAL 2.9 25.6 + - - -
34C ARG* 3.6 31.5 + - + +
35C LEU* 1.3 75.9 - - - +
37C LEU* 1.3 63.4 + - - +
60C LYS* 3.4 9.0 - - + -
62C TYR* 3.8 23.3 - - + +
70C ASP 5.0 1.3 - - - +
71C CYS* 2.8 35.9 + - - +
75C CYS* 3.7 4.3 - - - -
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Residues in contact with LEU 37 (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 VAL* 3.7 4.9 - - + -
14C ALA* 3.7 13.0 - - + -
23C SER* 3.1 25.6 - - - +
35C LEU* 3.7 28.3 - - + -
36C THR* 1.3 80.0 - - - +
38C TYR* 1.3 57.9 + - - +
43C THR* 3.5 7.8 - - + +
46C VAL* 3.9 19.3 - - + -
47C ALA* 4.1 9.4 - - + +
50C LEU* 3.8 25.8 - - + -
59C VAL* 4.0 14.8 - - + -
60C LYS 2.8 14.3 + - - +
61C GLY* 4.4 1.3 - - - -
62C TYR* 2.7 35.7 + - - +
71C CYS* 3.8 1.5 - - - -
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Residues in contact with TYR 38 (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 VAL 2.9 6.7 + - - -
12C LEU* 3.6 26.2 - - + -
13C GLY 2.7 30.1 + - - -
14C ALA* 3.0 7.8 + - - +
37C LEU* 1.3 74.3 - - - +
39C ASP* 1.3 72.3 + - - +
40C ILE* 3.8 6.4 - - - +
43C THR* 3.8 2.5 - - - -
62C TYR* 3.4 15.3 - - + -
63C LEU 4.3 0.4 - - - -
64C GLY* 3.2 40.7 - - - -
65C PRO* 3.2 13.9 - - - +
68C LEU* 3.6 42.8 - - + +
71C CYS* 3.7 7.4 - - - -
106C LEU* 4.0 9.4 - - + +
3002C NAD 3.4 30.9 + + - -
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Residues in contact with ASP 39 (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 GLY* 3.2 10.4 - - - -
15C SER* 3.0 25.7 + - - +
38C TYR* 1.3 83.4 - - - +
40C ILE* 1.3 75.0 + - - +
41C ALA* 3.2 24.3 + - - +
43C THR* 3.4 5.8 + - + +
62C TYR 3.3 5.1 + - - +
63C LEU* 3.4 8.5 - - - -
64C GLY 3.1 20.3 + - - -
3002C NAD 2.5 55.2 + - - -
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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