Contacts of the strand formed by residues 6 - 13 (chain D) in PDB entry 1DTJ
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 GLU 6 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.7 22.1 - - + +
9C GLU 3.5 14.1 - - - +
10C MET* 4.6 6.1 - - + +
69C GLN* 3.0 35.8 - - - +
5D LYS* 1.3 76.2 - - - +
7D LEU* 1.3 60.8 + - - +
8D VAL* 3.8 1.9 - - - +
58D ILE 3.9 0.3 - - - +
59D THR* 3.3 6.6 - - - -
60D GLY 2.7 36.3 + - - +
62D PRO* 3.4 25.9 - - + +
65D THR* 3.7 25.7 + - + +
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Residues in contact with LEU 7 (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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7C LEU* 4.7 0.7 - - + -
8C VAL* 3.2 5.9 - - - +
9C GLU* 2.8 55.9 + - + +
6D GLU* 1.3 76.7 - - - +
8D VAL* 1.3 64.3 + - - +
9D GLU* 3.2 44.4 - - + +
57D THR* 3.8 16.8 - - + -
58D ILE 3.5 4.5 - - - -
59D THR* 3.7 17.7 - - + -
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Residues in contact with VAL 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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6C GLU* 3.7 34.1 - - + +
7C LEU 3.2 7.6 - - - +
8C VAL* 4.0 10.1 - - + -
6D GLU* 3.8 9.9 - - - +
7D LEU* 1.3 78.9 - - - +
9D GLU* 1.3 70.7 + - - +
10D MET* 5.5 1.6 - - + -
56D VAL 3.7 0.7 - - - +
57D THR* 3.5 3.3 - - - -
58D ILE* 2.9 45.4 + - + +
65D THR* 2.7 39.9 - - + -
69D GLN* 4.7 8.7 - - + -
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Residues in contact with GLU 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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6C GLU* 3.6 5.0 - - - +
7C LEU* 2.7 58.5 + - + +
9C GLU* 3.7 10.4 - - - +
7D LEU* 3.2 34.5 - - + +
8D VAL* 1.3 75.4 - - - +
10D MET* 1.3 63.7 + - - +
55D ARG* 2.4 52.9 + - - +
56D VAL 3.3 3.4 - - - -
57D THR* 3.7 9.4 + - - +
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Residues in contact with MET 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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4C MET* 3.6 31.0 - - + -
5C LYS 4.9 3.6 - - - +
6C GLU* 4.7 6.1 - - + +
8D VAL* 5.5 1.1 - - + -
9D GLU* 1.3 78.2 - - - +
11D ALA* 1.3 62.0 + - - +
12D VAL* 4.1 13.2 - - + -
55D ARG* 3.6 3.9 - - - +
56D VAL* 2.7 46.6 + - + +
58D ILE* 4.2 14.8 - - + -
69D GLN* 4.1 23.6 - - - -
72D ILE* 3.7 32.1 - - + -
73D SER* 3.9 11.4 - - - +
76D VAL* 5.1 2.7 - - + -
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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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4C MET* 6.0 0.7 - - - +
5C LYS 5.4 2.2 + - - -
10D MET* 1.3 77.2 - - - +
12D VAL* 1.3 63.9 + - - +
13D PRO* 4.5 2.7 - - - +
53D ASN* 4.0 25.4 - - + +
54D ARG 3.5 5.6 - - - +
55D ARG* 4.8 1.8 - - - +
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Residues in contact with VAL 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 MET* 4.1 16.8 - - + +
11D ALA* 1.3 78.3 - - - +
13D PRO* 1.3 81.2 - - + +
16D LEU* 4.3 2.5 - - + -
17D VAL* 4.0 15.0 - - + +
20D ILE* 3.8 25.1 - - + -
53D ASN* 3.8 2.2 - - - -
54D ARG* 2.7 38.8 + - - +
56D VAL* 3.7 27.6 - - + -
76D VAL* 4.0 21.3 - - + -
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Residues in contact with PRO 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 4.5 3.1 - - - +
12D VAL* 1.3 92.8 - - + +
14D GLU* 1.3 63.4 + - - +
15D ASN* 2.9 13.9 + - + -
16D LEU* 2.9 39.9 + - + -
17D VAL* 3.3 9.0 + - - +
52D ARG* 3.6 4.5 - - + +
53D ASN* 3.3 20.8 - - - +
76D VAL* 4.5 8.3 - - + -
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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