Contacts of the strand formed by residues 7 - 14 (chain D) in PDB entry 1D1T
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 ILE 7 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D THR* 4.0 19.7 - - + +
5D LYS* 4.3 0.4 - - + +
6D VAL* 1.3 75.4 - - - +
8D LYS* 1.3 75.7 + - - +
9D CYS* 4.0 3.3 + - + -
26D ILE 3.6 0.3 - - - +
27D GLU* 3.2 4.9 - - - -
28D VAL* 2.7 43.3 + - + +
37D ARG* 3.4 27.8 - - - +
74D GLU* 3.4 22.9 - - - +
149D TYR* 3.8 49.8 - - + -
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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 VAL* 4.0 8.2 + - + +
7D ILE* 1.3 79.1 - - - +
9D CYS* 1.3 63.3 + - - +
25D GLU* 4.5 15.5 - - + +
26D ILE 3.3 6.1 - - - +
27D GLU* 4.2 23.6 - - + +
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Residues in contact with CYS 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 ILE* 4.2 1.6 - - + -
8D LYS* 1.3 77.0 - - - +
10D LYS* 1.3 63.5 + - - +
25D GLU* 3.3 12.0 + - - -
26D ILE* 2.7 38.9 + - - +
28D VAL* 3.9 28.0 - - - -
147D THR* 3.9 16.8 - - - -
148D GLU* 3.2 30.7 - - + +
149D TYR* 4.0 15.7 - - + -
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Residues in contact with LYS 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 CYS* 1.3 78.3 - - - +
11D ALA* 1.3 61.2 + - - +
23D ILE* 4.2 19.2 - - + +
24D GLU 3.2 11.7 - - - +
25D GLU* 4.1 24.0 - - - +
147D THR* 3.6 1.2 + - - -
148D GLU* 3.0 43.0 + - + +
352D PHE* 4.8 9.2 - - + -
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Residues in contact with ALA 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 CYS 4.0 0.4 + - - -
10D LYS* 1.3 74.5 - - - +
12D ALA* 1.3 59.5 + - - +
13D VAL* 3.0 11.6 + - - +
23D ILE* 4.3 3.1 - - - +
24D GLU 3.1 26.0 + - - +
26D ILE* 3.6 26.0 - - + -
64D ILE* 3.8 11.9 - - + -
146D PHE 3.5 5.8 - - - +
147D THR* 3.4 26.0 - - - +
352D PHE* 4.6 2.9 - - - -
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Residues in contact with ALA 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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11D ALA* 1.3 67.4 - - - +
13D VAL* 1.3 62.4 + - - +
21D PHE* 4.0 27.6 - - + -
22D SER 3.8 4.9 - - - -
23D ILE* 4.2 9.9 - - + -
63D VAL 4.4 0.2 - - - +
64D ILE* 3.9 20.6 - - - +
65D VAL 4.6 0.3 + - - -
146D PHE* 2.8 21.8 + - + +
352D PHE* 3.5 25.6 - - + -
355D ILE* 4.0 9.2 - - + -
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Residues in contact with VAL 13 (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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11D ALA* 3.3 17.0 - - + +
12D ALA* 1.3 74.6 - - - +
14D LEU* 1.3 70.3 + - - +
15D TRP* 3.9 19.5 - - + +
20D PRO 4.1 0.5 - - - +
21D PHE* 3.4 7.1 - - - -
22D SER* 2.7 45.7 + - - +
24D GLU* 3.6 22.7 - - + -
26D ILE* 4.1 15.7 - - + -
62D PRO* 4.0 24.9 - - + -
63D VAL 3.9 8.3 - - - +
64D ILE* 4.6 4.7 - - + -
132D CYS* 4.8 2.2 - - + -
137D VAL* 4.5 11.4 - - + -
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Residues in contact with LEU 14 (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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13D VAL* 1.3 73.7 - - - +
15D TRP* 1.3 64.6 + - - +
16D GLU 3.2 5.8 - - - +
19D GLN 3.7 14.8 - - - +
20D PRO 3.5 19.7 - - - +
21D PHE* 3.3 42.0 - - + -
52D VAL* 3.7 28.7 - - + -
53D ILE* 4.0 18.2 - - + +
61D PHE* 3.2 12.1 - - + -
63D VAL* 3.0 37.1 + - + +
65D VAL* 4.1 13.0 - - + -
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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