Contacts of the strand formed by residues 404 - 409 (chain A) in PDB entry 1D7K
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 THR 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASP* 6.2 2.0 - - + -
39A ALA 3.9 4.1 + - - +
40A PHE* 3.6 10.5 - - + +
41A TYR 3.1 21.1 + - - +
402A ARG 3.5 4.6 + - - -
403A PRO* 1.3 72.1 - - - +
405A ILE* 1.3 60.5 + - - +
406A TYR* 3.6 33.3 + - + +
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Residues in contact with ILE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.0 13.9 - - - +
41A TYR* 3.8 28.0 - - + -
43A ALA* 3.8 20.6 - - + -
73A SER* 4.3 8.7 - - - +
284A PHE* 4.0 15.0 - - + -
391A VAL* 4.5 13.7 - - + -
403A PRO 3.6 5.4 + - - +
404A THR* 1.3 78.9 + - - +
406A TYR* 1.3 66.8 + - - +
407A TYR* 3.5 45.5 + - + +
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Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 3.0 30.1 - - - -
12A HIS* 5.5 4.7 - + - +
23A ILE* 6.1 0.4 - - + -
27A LYS* 3.6 46.9 + - + +
40A PHE* 4.1 12.8 - + + -
41A TYR 2.9 23.1 + - - +
42A VAL* 3.8 10.1 - - + +
43A ALA 3.1 21.0 + - - -
404A THR* 3.6 32.6 + - + +
405A ILE* 1.3 76.1 - - - +
407A TYR* 1.3 63.4 + - - +
408A VAL* 3.6 4.7 + - + +
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Residues in contact with TYR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 4.0 20.2 - + + -
10A ASP 2.8 24.8 + - - +
11A CYS* 3.3 18.6 - - + -
12A HIS* 3.0 26.9 + - - +
43A ALA* 3.5 26.2 - - + -
45A LEU* 3.8 26.0 - - + -
73A SER* 3.2 31.2 + - - -
75A ALA* 3.8 21.7 + - + -
76A ILE* 4.2 9.2 - - + -
284A PHE* 4.2 2.6 - + - -
405A ILE* 3.5 34.1 - - + +
406A TYR* 1.3 71.6 - - - +
408A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A CYS* 4.4 2.2 - - - -
12A HIS* 3.3 14.6 - - + +
14A LEU* 3.5 31.9 - - + -
20A ALA* 4.2 9.2 - - + -
23A ILE* 4.2 22.9 - - + -
42A VAL* 4.2 18.6 - - + -
43A ALA 3.0 13.9 + - - +
44A ASP* 3.5 15.7 - - - +
45A LEU* 3.0 27.4 + - - +
406A TYR* 3.6 5.4 + - + +
407A TYR* 1.3 77.6 - - - +
409A MET* 1.3 64.0 + - - +
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Residues in contact with MET 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A CYS* 4.6 5.4 - - - -
12A HIS 3.0 8.7 + - - -
13A PHE* 3.3 21.1 - - + -
14A LEU* 3.1 22.7 + - - +
44A ASP* 4.4 5.4 - - - -
45A LEU* 4.1 19.7 - - + +
46A GLY 4.1 4.3 - - - +
49A LEU* 3.8 13.2 - - + -
408A VAL* 1.3 79.4 - - - +
410A SER* 1.3 74.3 + - - +
413A ALA* 3.6 31.9 - - + +
414A TRP* 3.9 22.9 - - + -
417A MET* 3.1 37.0 - - + -
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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