Contacts of the strand formed by residues 2 - 7 (chain E) in PDB entry 4GTU
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 MET 2 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E SER* 1.3 73.5 - - - +
3E THR* 1.3 59.7 + - - +
20E LEU* 5.1 1.8 - - + -
25E SER* 4.3 20.0 - - - +
26E SER* 2.8 38.1 + - - +
27E TYR* 2.9 13.3 - - + +
28E GLU 2.7 22.1 + - - -
62E LEU* 4.0 20.4 - - + -
63E ILE 3.4 18.6 - - - +
64E ASP* 3.3 35.2 - - + +
65E GLY 5.1 2.0 - - - +
78E TYR* 5.0 9.2 - - + -
79E ILE* 5.1 13.2 - - + -
82E LYS* 5.3 7.9 - - + +
83E HIS* 6.1 0.2 - - - +
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Residues in contact with THR 3 (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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1E SER 3.7 1.5 + - - -
2E MET* 1.3 74.0 - - - +
4E LEU* 1.3 68.1 + - - +
28E GLU* 3.6 19.6 - - - +
30E LYS* 2.9 37.3 + - - +
61E TYR* 3.6 1.6 - - + +
62E LEU* 3.5 11.8 - - - +
63E ILE* 3.2 65.3 + - + +
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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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2E MET 3.9 0.6 + - - -
3E THR* 1.3 80.9 + - - +
5E GLY* 1.3 69.7 + - - +
6E TYR* 4.2 21.3 - - + +
13E ALA* 4.7 5.8 - - + -
16E ILE* 3.6 33.4 - - + -
17E ARG* 4.7 18.8 - - + +
20E LEU* 3.8 20.4 - - + -
27E TYR* 4.4 6.5 - - + +
28E GLU 2.8 19.5 + - - +
29E GLU* 4.4 11.7 - - + +
30E LYS* 2.9 24.6 + - - +
60E PRO* 5.0 2.9 - - + -
61E TYR* 4.0 4.7 - - - +
62E LEU* 4.4 11.2 - - + -
75E ILE* 5.4 0.9 - - + -
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Residues in contact with GLY 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 78.6 - - - +
6E TYR* 1.3 54.5 + - - -
30E LYS* 3.6 8.1 - - - -
32E TYR* 4.4 0.7 - - - -
59E LEU* 3.1 9.2 - - - +
60E PRO* 2.8 36.6 - - - +
61E TYR* 3.2 35.0 + - - -
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Residues in contact with TYR 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* 4.2 7.2 - - + +
5E GLY* 1.3 73.2 - - - +
7E TRP* 1.3 94.5 + + - +
9E ILE* 3.3 27.5 - - + +
10E ARG 3.4 12.1 - - - -
11E GLY* 3.8 7.8 - - - -
12E LEU* 3.2 29.5 + - + +
13E ALA* 3.5 9.9 - - + -
17E ARG* 3.4 22.4 - - - +
30E LYS 2.9 19.6 + - - +
31E LYS* 3.3 1.1 - - - -
32E TYR* 2.9 18.1 + - - -
59E LEU* 3.2 15.4 - - + +
60E PRO* 3.3 37.9 - - + -
209E THR* 5.6 3.1 - - - +
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Residues in contact with TRP 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 TYR* 1.3 119.5 + + - +
8E ASP* 1.3 59.8 + - - +
9E ILE* 2.9 30.5 + - + +
17E ARG* 4.7 0.9 + - - -
31E LYS* 4.1 7.0 - - - +
32E TYR* 3.1 32.8 - - + +
33E THR 4.9 1.8 - - - -
34E MET* 3.8 20.2 - - + -
42E ARG* 3.4 53.8 - - + -
44E GLN* 6.3 0.4 - - + -
45E TRP* 4.2 19.1 - + + -
59E LEU* 3.4 28.6 + - + +
203E LEU* 4.7 4.2 - - - +
209E THR* 4.4 18.2 - - + +
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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