Contacts of the strand formed by residues 3 - 8 (chain e) in PDB entry 5GJQ
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 THR 3 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1e THR* 4.1 7.4 - - + -
2e THR* 1.3 79.4 - - - +
4e LEU* 1.3 62.3 + - - +
15e ALA 3.4 7.0 - - - -
16e ALA* 3.8 15.5 - - + -
33e LYS* 4.6 4.3 - - + -
44e THR* 4.0 16.7 + - - +
45e MET 3.8 22.2 - - - +
46e ALA* 4.8 0.9 - - + +
100e MET* 3.3 19.9 - - - +
127e SER* 3.0 10.1 + - - -
128e VAL* 2.8 43.9 + - - +
160e ILE* 4.4 1.6 - - - -
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Residues in contact with LEU 4 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3e THR* 1.3 75.8 - - - +
5e ALA* 1.3 67.5 + - - +
6e PHE* 3.9 17.0 - - + -
13e ILE 4.9 1.1 - - - +
14e VAL* 3.7 2.4 - - - +
15e ALA* 2.9 35.4 + - + +
100e MET* 3.7 7.4 - - - +
126e PHE 3.2 13.9 - - - +
127e SER* 4.1 8.1 - - - +
135e ALA* 4.2 8.1 - - + -
139e MET* 3.8 21.1 - - - -
156e ALA* 4.0 18.4 - - + +
159e ALA* 3.6 30.5 - - + -
160e ILE* 3.6 27.8 - - + +
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Residues in contact with ALA 5 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4e LEU* 1.3 77.7 - - - +
6e PHE* 1.3 64.5 + - - +
12e VAL* 4.6 1.1 - - + -
13e ILE 3.1 13.7 - - - +
14e VAL* 4.0 5.2 - - + -
100e MET* 3.6 19.9 - - + -
102e CYS* 3.9 12.6 - - - -
111e LEU* 3.6 19.2 - - + +
125e THR* 3.4 0.9 - - - -
126e PHE 2.8 31.5 + - - +
139e MET* 4.8 0.6 - - - +
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Residues in contact with PHE 6 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4e LEU* 3.9 14.8 - - + -
5e ALA* 1.3 75.1 - - - +
7e LYS* 1.3 58.7 + - - +
8e PHE* 4.3 13.4 - + - -
11e GLY 4.1 0.3 - - - +
12e VAL* 3.4 4.4 - - - -
13e ILE* 2.9 54.2 + - + -
111e LEU* 4.1 0.7 - - - -
124e ALA 3.3 4.9 - - - -
125e THR* 3.6 24.9 - - + -
139e MET* 3.9 12.1 - - + -
143e TYR* 3.6 23.6 - + + -
147e LEU* 4.7 3.6 - - + -
152e ALA* 3.5 35.0 - - + -
155e LEU* 4.4 12.3 - - + -
156e ALA* 3.8 27.6 - - + -
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Residues in contact with LYS 7 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6e PHE* 1.3 73.1 - - - +
8e PHE* 1.3 56.4 + - - +
11e GLY 3.2 11.4 - - - +
12e VAL* 3.7 15.9 - - + -
109e PRO* 3.6 34.0 + - + +
110e GLY* 4.7 4.2 - - - +
111e LEU* 4.2 8.2 - - + +
122e SER* 4.1 13.7 + - - -
123e GLY 3.3 27.2 + - - +
124e ALA* 2.9 21.2 + - + +
143e TYR* 2.4 31.7 + - - -
145e TYR* 3.9 12.1 - - + -
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Residues in contact with PHE 8 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6e PHE* 4.3 10.1 - + + -
7e LYS* 1.3 76.7 - - - +
9e ARG* 1.3 72.4 + - - +
10e HIS* 3.2 23.1 + - + -
11e GLY* 3.0 36.1 + - - +
12e VAL 4.2 0.2 - - - -
13e ILE* 3.8 24.7 - - + -
109e PRO* 4.3 7.4 - - - +
143e TYR* 4.4 5.6 - - + +
144e SER 4.0 10.3 - - - +
145e TYR* 3.5 30.5 + - - +
147e LEU* 3.6 33.7 - - + -
148e GLU 4.2 5.6 - - - -
149e VAL* 4.8 2.7 - - - -
152e ALA* 3.4 27.8 - - + -
178e HIS* 4.4 5.6 - + - -
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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