Contacts of the strand formed by residues 7 - 12 (chain D) 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 ALA 7 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASN* 1.3 86.2 + - - +
8D LYS* 1.3 59.6 + - - +
9D VAL* 3.9 8.7 - - + -
31D LEU 3.0 11.2 + - - +
32D VAL* 3.5 5.7 - - - +
33D SER* 2.8 28.3 + - - +
34D ARG 3.5 3.3 + - - +
76D ASP* 3.6 16.6 - - + +
77D VAL* 5.2 0.2 - - + -
245D VAL* 3.8 26.5 - - + -
248D MET* 5.9 2.0 - - + -
249D ASN* 6.0 0.2 - - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASN 4.6 4.0 - - - +
7D ALA* 1.3 72.6 - - - +
9D VAL* 1.3 61.0 + - - +
33D SER* 3.9 11.4 - - - +
34D ARG* 3.5 50.1 - - + +
74D GLY* 3.1 32.3 + - - +
75D CYS* 3.8 2.6 - - - -
76D ASP* 2.8 50.8 + - - +
77D VAL 3.2 8.0 + - - +
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA* 4.1 20.0 - - + +
8D LYS* 1.3 79.0 - - - +
10D ALA* 1.3 66.1 + - - +
26D LEU* 3.9 26.0 - - + -
32D VAL* 4.2 19.7 - - + -
34D ARG* 2.9 8.6 + - - +
35D LEU* 3.2 12.6 - - + +
36D THR* 2.8 32.1 + - - +
75D CYS* 4.5 1.3 - - - -
77D VAL* 3.3 18.8 - - + +
79D VAL* 4.1 12.6 - - + -
241D VAL* 4.5 11.9 - - + -
245D VAL* 4.9 0.9 - - + -
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Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 1.3 76.4 - - - +
11D VAL* 1.3 62.0 - - - +
12D LEU* 4.1 2.0 - - + -
36D THR* 3.1 21.5 - - - +
71D CYS* 4.0 12.3 - - - +
72D LEU* 4.3 4.5 - - + -
75D CYS* 3.6 16.1 - - - -
77D VAL 3.0 9.4 + - - +
78D VAL* 3.5 16.3 - - + -
79D VAL 2.9 26.2 + - - -
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Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.7 0.2 - - + -
10D ALA* 1.3 76.6 - - - +
12D LEU* 1.3 61.6 + - - +
14D ALA* 3.6 22.5 - - + +
19D GLY* 4.4 2.2 - - - -
22D LEU* 4.3 12.8 - - + -
23D SER* 3.8 19.5 - - - +
26D LEU* 3.5 32.5 - - + -
35D LEU* 4.0 9.0 - - + -
36D THR 2.9 9.3 + - - -
37D LEU* 3.7 4.8 - - + -
38D TYR* 2.9 30.1 + - - +
79D VAL* 3.4 4.3 - - + -
81D PRO* 3.9 23.8 - - + -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 4.4 2.2 - - + -
11D VAL* 1.3 72.8 - - - +
13D GLY* 1.3 58.5 + - - +
38D TYR* 3.7 27.4 - - + -
68D LEU* 4.0 9.6 - - + -
71D CYS* 4.2 6.5 - - - -
72D LEU* 3.8 20.6 - - + -
78D VAL* 3.6 27.8 - - + -
79D VAL 2.9 9.3 + - - +
80D ILE* 3.6 12.7 - - + -
81D PRO* 3.0 12.2 - - - +
82D ALA* 3.0 23.6 + - - +
106D LEU* 4.0 35.2 - - + +
110D CYS* 4.0 15.0 - - - -
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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