Contacts of the strand formed by residues 7 - 16 (chain T) in PDB entry 3HOU
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 7 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T THR* 4.9 5.8 - - + +
6T PHE* 1.3 84.3 - - - +
8T ASP* 1.3 84.7 + - - +
9T ILE* 5.7 0.7 - - - +
56T THR* 4.1 11.3 - - - +
57T VAL 3.5 12.8 - - - +
58T THR* 4.1 13.1 + - - +
93T TYR* 4.6 3.8 + - - -
129T TYR* 6.0 0.5 - - - -
145T ARG* 4.8 7.7 + - - -
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Residues in contact with ASP 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T PHE* 3.9 8.3 - - + -
7T ASP* 1.3 88.4 + - - +
9T ILE* 1.3 101.4 + - - +
10T PHE* 3.6 20.1 - - + -
30T SER* 2.5 28.1 + - - -
31T THR 4.1 0.5 + - - -
32T THR* 3.9 17.2 + - - -
33T GLN* 4.9 0.9 + - - +
36T CYS* 4.4 5.5 - - - +
56T THR* 3.5 2.5 - - - +
57T VAL 2.8 29.5 + - - +
129T TYR* 5.1 3.1 + - - -
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Residues in contact with ILE 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T ASP* 5.7 0.4 - - - +
8T ASP* 1.3 102.7 + - - +
10T PHE* 1.3 73.5 + - - +
30T SER* 3.7 0.7 - - - -
31T THR* 3.1 31.2 + - - +
54T SER* 3.9 15.7 - - - -
55T LEU 3.1 18.2 - - - +
56T THR* 3.7 16.4 - - + +
146T ARG* 3.9 17.5 - - - +
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Residues in contact with PHE 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T PHE* 3.6 15.3 - + - -
8T ASP* 3.6 20.4 - - + -
9T ILE* 1.3 79.7 - - - +
11T GLN* 1.3 63.2 + - - +
28T ALA* 3.7 28.9 - - + -
29T ALA 3.0 17.5 - - - +
30T SER* 3.8 2.7 - - - -
31T THR* 4.5 2.9 - - - -
36T CYS* 3.3 36.3 - - - -
37T LYS 4.3 1.1 - - - -
38T LEU* 3.9 23.3 - - + -
53T ASP 2.9 12.0 - - - +
54T SER* 3.4 4.9 - - - -
55T LEU* 3.0 20.8 + - + +
57T VAL* 3.5 37.5 - - + -
125T LEU* 4.2 6.5 - - + -
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Residues in contact with GLN 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T PHE* 1.3 74.6 - - - +
12T VAL* 1.3 59.0 + - - +
13T SER* 2.9 9.0 + - - -
28T ALA* 2.7 20.6 - - - +
29T ALA* 3.0 15.6 + - + +
31T THR* 5.0 6.1 - - - +
52T GLN* 3.2 37.3 + - - +
53T ASP* 3.0 16.0 - - - +
54T SER* 5.2 2.7 - - - +
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Residues in contact with VAL 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T GLN* 1.3 69.3 - - - +
13T SER* 1.3 68.2 + - - +
14T GLU 3.9 11.0 - - - +
15T VAL* 3.5 32.5 - - + -
26T ILE* 4.0 14.1 - - + -
28T ALA* 3.3 10.6 - - + +
49T VAL* 3.9 7.0 - - + -
50T ALA 4.2 0.2 - - - +
51T ALA* 3.9 5.4 - - - -
52T GLN* 2.8 37.8 + - - +
53T ASP* 3.3 20.9 + - + +
55T LEU* 3.4 32.1 - - + -
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Residues in contact with SER 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T GLN 2.9 7.2 + - - -
12T VAL* 1.3 74.7 - - - +
14T GLU* 1.3 61.5 + - - +
27T GLU* 2.6 26.8 + - - -
28T ALA* 4.4 3.8 - - - -
29T ALA 5.4 0.7 - - - -
51T ALA* 3.8 8.8 - - - +
52T GLN* 5.5 3.3 + - - +
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Residues in contact with GLU 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T VAL* 3.3 1.9 - - - +
13T SER* 1.3 87.3 - - - +
15T VAL* 1.3 86.9 + - - +
16T ASP* 4.6 11.3 - - - +
25T ARG 3.8 1.7 - - - +
26T ILE* 3.6 3.1 - - - -
27T GLU* 3.2 28.8 + - + +
51T ALA* 4.1 11.7 - - + -
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Residues in contact with VAL 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T VAL* 3.5 15.7 - - + -
14T GLU* 1.3 86.3 - - - +
16T ASP* 1.3 63.3 + - - +
17T PRO* 3.9 5.6 - - + +
24T CYS* 3.3 31.9 - - + -
25T ARG 3.7 2.7 - - - -
26T ILE* 3.3 24.7 - - + -
44T VAL* 4.8 2.5 - - + -
49T VAL 3.0 31.6 - - - +
50T ALA* 5.1 0.7 - - - -
51T ALA* 3.9 11.2 - - - +
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Residues in contact with ASP 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T GLU* 4.6 12.3 - - - +
15T VAL* 1.3 77.2 - - - +
17T PRO* 1.3 81.3 - - - +
18T GLY* 3.2 19.7 + - - -
23T VAL 4.4 0.2 - - - +
24T CYS* 3.1 3.2 - - - -
25T ARG* 2.7 51.5 + - + +
27T GLU* 6.1 0.7 - - - +
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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