Contacts of the strand formed by residues 9 - 14 (chain M) in PDB entry 1GTN
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 PHE 9 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9L PHE* 5.6 1.4 - - - -
7M SER 4.6 3.1 - - - -
8M ASP* 1.3 82.7 + - - +
10M VAL* 1.3 70.6 + - - +
11M VAL* 3.8 16.2 - - + -
45M ILE* 3.4 21.8 - - + -
46M ALA 2.9 27.4 - - - +
47M GLN* 3.8 7.2 - - + +
48M PHE* 5.3 0.4 - - - -
64M GLN 4.5 0.2 - - - +
65M THR* 4.6 2.4 - - - -
66M ARG 5.0 0.2 + - - -
8N ASP* 3.5 31.0 - - + -
9N PHE 5.6 1.8 - - - -
10N VAL* 5.3 3.6 - - + -
48N PHE* 3.9 19.7 - + + -
65N THR* 3.9 19.5 - - - -
66N ARG* 4.4 9.6 - - + -
67N HIS* 3.3 43.8 + + - -
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Residues in contact with VAL 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L PHE* 5.1 1.8 - - + -
45L ILE* 3.9 39.5 - - + -
9M PHE* 1.3 84.1 - - - +
11M VAL* 1.3 58.5 + - - +
12M ILE* 3.8 26.6 - - + +
44M LEU 3.8 1.0 - - - +
45M ILE* 3.6 3.3 - - - -
46M ALA* 2.8 35.5 + - + +
48M PHE* 4.4 12.3 - - + -
55M ILE* 3.9 21.8 - - + -
63M ILE* 4.9 1.3 - - + -
64M GLN 3.6 7.2 - - - +
65M THR* 4.0 12.1 - - + -
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Residues in contact with VAL 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M PHE* 3.8 26.5 - - + -
10M VAL* 1.3 70.7 - - - +
12M ILE* 1.3 66.3 + - - +
43M VAL* 3.8 22.7 - - + -
44M LEU 3.7 3.8 - - - -
45M ILE* 4.2 8.7 - - + -
62M TYR 3.7 1.0 - - - +
63M ILE* 3.4 3.5 - - - +
64M GLN* 2.7 68.8 + - + +
65N THR* 4.0 17.9 - - + +
67N HIS* 5.0 1.3 - - + -
70N ILE* 4.1 19.7 - - + -
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Residues in contact with ILE 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L ILE* 5.6 0.4 - - + -
10M VAL* 3.8 25.8 - - + -
11M VAL* 1.3 79.6 - - - +
13M LYS* 1.3 61.0 + - - +
14M ALA 4.2 0.2 + - - -
19M VAL* 5.0 0.7 - - + -
21M VAL* 3.7 36.1 - - + -
38M LEU* 4.1 19.8 - - + +
42M GLU 3.8 1.0 - - - +
43M VAL* 3.2 7.9 - - - -
44M LEU* 2.9 46.1 + - + +
46M ALA* 5.9 1.6 - - + -
55M ILE* 4.6 1.3 - - + -
57M VAL* 4.0 17.0 - - + -
61M ALA* 4.0 22.2 - - + -
62M TYR 3.5 3.6 - - - +
63M ILE* 4.2 13.7 - - + -
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Residues in contact with LYS 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ILE* 1.3 72.5 - - - +
14M ALA* 1.3 69.8 + - - +
15M LEU* 3.3 17.8 + - + +
41M GLY* 4.2 17.9 - - - +
42M GLU 3.6 9.0 - - - +
43M VAL* 4.2 7.9 - - + +
61M ALA* 3.2 6.9 - - - +
62M TYR* 2.8 44.9 + - + +
70N ILE* 3.7 27.9 - - + +
71N GLU* 2.9 30.9 + - - +
73N GLU* 2.9 29.6 + - - +
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Residues in contact with ALA 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ILE 4.2 1.0 + - - -
13M LYS* 1.3 75.4 - - - +
15M LEU* 1.3 60.0 + - - +
16M GLU 3.8 2.2 - - - +
19M VAL* 3.8 25.4 - - + -
38M LEU* 3.9 17.6 - - + +
39M ASP 3.3 31.2 - - - +
40M LYS* 4.2 0.3 - - - +
41M GLY* 2.8 26.4 + - - -
42M GLU 3.1 10.5 + - - +
60M LYS 4.2 0.2 - - - -
61M ALA* 4.3 1.1 - - - -
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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