Contacts of the strand formed by residues 3 - 14 (chain J) in PDB entry 1DM0
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 ASP 3 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J PRO* 1.3 76.8 - - - +
4J CYS* 1.3 59.4 + - - +
5J VAL 4.9 1.8 - - - +
6J THR* 4.6 5.7 + - - +
51J THR* 3.7 21.8 - - + +
52J ILE 3.9 0.9 - - - -
53J LYS* 2.4 40.4 + - - +
54J THR 4.8 0.5 - - - +
67J ILE* 5.2 0.6 - - - +
69J ARG* 4.9 5.5 + - - -
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Residues in contact with CYS 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J PRO 3.1 0.8 + - - -
3J ASP* 1.3 73.0 - - - +
5J VAL* 1.3 72.4 + - - +
27J LYS* 4.7 2.6 + - - -
29J LEU* 4.5 11.7 - - - -
52J ILE 3.0 9.8 + - - +
54J THR* 3.4 40.2 - - + +
57J CYS* 2.0 73.2 - - - -
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Residues in contact with VAL 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J ASP* 3.8 0.8 - - - +
4J CYS* 1.3 87.9 - - - +
6J THR* 1.3 65.8 + - - +
24J VAL* 3.2 42.6 - - + +
25J GLY* 4.2 7.0 - - - -
26J ASP* 3.5 25.6 - - - +
27J LYS* 4.2 5.4 - - + +
29J LEU* 4.5 10.1 - - + -
51J THR* 4.0 0.2 - - - +
52J ILE* 2.7 42.8 + - + +
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Residues in contact with THR 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J ASP* 4.6 6.8 + - - +
5J VAL* 1.3 81.4 + - - +
7J GLY* 1.3 60.1 + - - +
24J VAL* 3.7 3.6 - - - -
25J GLY* 5.0 5.3 + - - -
49J THR* 4.4 14.6 - - + -
50J VAL 3.2 9.2 - - - +
51J THR* 3.1 31.6 + - - +
69J ARG* 4.6 4.0 - - - +
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Residues in contact with GLY 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J THR* 1.3 78.0 - - - +
8J LYS* 1.3 68.4 + - - -
9J VAL 3.8 0.3 + - - -
24J VAL* 3.2 11.3 - - - +
25J GLY* 4.8 4.7 - - - -
49J THR* 4.6 7.9 - - - -
50J VAL* 3.0 28.4 + - - +
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Residues in contact with LYS 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J GLY* 1.3 77.8 - - - -
9J VAL* 1.3 65.5 + - - +
10J GLU* 3.4 5.1 + - - +
24J VAL* 4.0 9.9 - - - +
25J GLY 4.4 1.9 + - - -
47J GLY* 3.6 24.5 - - - +
48J MET 3.8 12.3 - - - +
49J THR* 2.8 30.0 + - - +
273L ASN* 3.9 12.4 - - - +
274L LYS* 5.3 9.7 - - - +
275L ILE* 6.1 2.7 - - + -
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Residues in contact with VAL 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LYS* 1.3 74.6 - - - +
10J GLU* 1.3 66.1 + - - +
11J TYR 4.0 7.2 - - - +
12J THR* 4.0 3.8 - - + -
22J VAL* 3.2 35.4 - - + -
23J LYS 3.9 3.6 - - - +
24J VAL* 4.2 2.2 - - + -
40J LEU* 4.7 9.0 - - + +
43J ALA* 4.9 0.9 - - + -
44J GLN* 3.7 52.9 + - + +
48J MET 4.5 3.3 + - - +
50J VAL* 4.1 31.2 - - + -
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Residues in contact with GLU 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I ARG* 4.0 12.5 - - - +
8J LYS 3.4 4.9 + - - +
9J VAL* 1.3 74.0 - - - +
11J TYR* 1.3 68.0 + - + +
23J LYS* 2.8 50.9 + - + +
24J VAL* 5.5 0.2 - - - -
25J GLY* 3.6 13.2 + - - +
44J GLN* 4.0 4.7 + - - -
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Residues in contact with TYR 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I ILE* 4.2 14.1 - - + -
68I PHE 3.2 17.9 - - - +
69I ARG* 4.0 31.0 - - + -
9J VAL* 3.5 3.1 - - - +
10J GLU* 1.3 86.2 - - + +
12J THR* 1.3 72.7 + - - +
13J LYS* 4.5 13.0 - - + -
21J THR* 4.5 4.3 - - + -
22J VAL* 3.7 0.5 - - - -
23J LYS* 3.0 59.0 + - + +
28J GLU* 2.8 38.0 + - - -
44J GLN* 3.4 5.6 - - - +
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Residues in contact with THR 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I ILE* 3.5 2.1 - - - +
68I PHE* 2.8 31.5 + - - +
9J VAL* 4.0 3.1 - - + -
11J TYR* 1.3 74.6 - - - +
13J LYS* 1.3 64.0 + - - +
14J TYR 4.3 0.4 - - - -
20J PHE* 3.0 39.5 - - + -
21J THR 3.2 4.9 - - - -
22J VAL* 3.4 25.4 - - + -
40J LEU* 4.9 6.3 - - + -
41J LEU* 3.5 12.0 - - + +
44J GLN* 2.5 28.1 + - - +
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Residues in contact with LYS 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I LYS* 4.8 4.7 - - - +
65I GLU* 3.2 27.5 + - - -
66I VAL 3.1 14.4 - - - +
67I ILE* 3.6 31.0 - - + -
68I PHE* 4.6 0.7 - - - +
11J TYR* 4.5 8.5 - - + -
12J THR* 1.3 77.1 - - - +
14J TYR* 1.3 66.6 + - - +
15J ASN* 2.9 33.3 + - - +
20J PHE* 4.9 1.3 - - - -
21J THR* 2.7 34.6 + - + +
28J GLU* 4.5 15.1 + - - +
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Residues in contact with TYR 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ARG* 3.6 24.8 + - + +
35I ASN* 4.1 20.9 + - + -
36I LEU* 3.3 33.9 - - + -
39I LEU* 4.6 1.1 - - + -
64I SER 3.3 19.7 - - - -
65I GLU* 3.1 5.9 - - - +
66I VAL* 3.0 30.5 + - + +
68I PHE* 4.7 8.4 - - + -
12J THR 4.3 0.4 - - - -
13J LYS* 1.3 69.2 - - - +
15J ASN* 1.3 85.9 + - - +
18J ASP* 3.0 33.6 + - - +
19J THR 3.9 6.7 - - - -
20J PHE* 4.2 27.1 - + + -
37J GLN* 4.4 19.3 - - - -
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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