Contacts of the helix formed by residues 5 - 13 (chain E) in PDB entry 5D4E
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 GLY 5 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925D GLU* 3.3 16.2 + - - -
4E PRO* 1.3 72.2 - - - +
6E ILE* 1.3 59.1 + - - +
7E ASP* 3.2 3.8 - - - -
8E LYS* 3.3 10.4 + - - +
9E LEU* 3.0 32.0 + - - +
69E LEU* 3.9 13.2 - - - +
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Residues in contact with ILE 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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761D ILE* 4.3 8.1 - - + -
767D HIS* 3.5 36.8 - - + +
924D MET* 3.9 16.2 - - + -
925D GLU* 4.4 7.8 + - + +
2E ALA* 5.1 0.9 - - + -
3E GLU* 3.3 22.9 - - + +
4E PRO 3.2 2.5 - - - -
5E GLY* 1.3 73.4 - - - +
7E ASP* 1.3 73.0 + - - +
9E LEU* 3.4 10.7 + - + -
10E PHE* 2.9 65.7 + - + -
19E LEU* 4.4 7.4 - - + -
65E MET* 4.8 3.6 - - + -
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Residues in contact with ASP 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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922D LEU 5.2 1.9 - - - +
923D GLY* 3.5 11.3 - - - -
924D MET* 3.2 30.2 + - - +
925D GLU* 3.7 31.0 + - - +
1213D ARG* 4.7 15.2 + - - +
5E GLY* 3.2 1.1 - - - -
6E ILE* 1.3 80.0 - - - +
8E LYS* 1.3 57.4 + - - +
10E PHE* 3.4 9.2 + - - +
11E GLY* 2.9 23.7 + - - -
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Residues in contact with LYS 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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5E GLY* 3.3 13.0 + - - +
7E ASP* 1.3 77.5 - - - +
9E LEU* 1.3 59.7 + - - +
11E GLY* 2.9 4.4 + - - +
12E MET* 2.9 52.6 + - + +
69E LEU* 3.7 32.6 + - + +
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Residues in contact with LEU 9 (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 PRO 4.6 6.3 - - - +
5E GLY 3.0 21.5 + - - +
6E ILE* 3.7 6.7 - - + +
7E ASP 3.3 0.2 - - - -
8E LYS* 1.3 76.8 - - - +
10E PHE* 1.3 62.3 + - - +
12E MET* 3.2 41.3 + - + +
13E VAL* 3.5 13.2 - - - +
19E LEU* 3.6 27.1 - - + +
65E MET* 3.6 44.9 - - + +
68E LEU* 4.1 26.2 - - + -
69E LEU* 4.1 13.0 - - + -
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Residues in contact with PHE 10 (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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761D ILE* 3.6 36.6 - - + -
767D HIS* 5.2 3.8 - + + -
924D MET* 4.0 26.7 - - + -
1211D MET* 4.5 11.2 - - - -
1213D ARG* 3.7 24.8 + - - +
6E ILE* 2.9 43.4 + - + +
7E ASP* 3.7 3.8 - - - +
9E LEU* 1.3 76.3 - - - +
11E GLY* 1.3 60.2 + - - +
13E VAL* 3.3 22.2 + - - +
16E LYS* 3.7 37.0 - - + -
19E LEU* 3.5 14.8 - - + -
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Residues in contact with GLY 11 (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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1213D ARG* 5.6 1.8 - - - -
7E ASP 2.9 14.6 + - - -
8E LYS* 2.9 7.1 + - - -
10E PHE* 1.3 79.1 - - - +
12E MET* 1.3 61.7 + - - +
13E VAL 3.4 3.5 + - - +
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Residues in contact with MET 12 (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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8E LYS* 2.9 42.0 + - + +
9E LEU* 3.2 27.7 + - + +
11E GLY* 1.3 77.8 - - - +
13E VAL* 1.3 60.6 + - + +
19E LEU* 6.1 0.7 - - + -
68E LEU* 3.3 38.4 - - - +
69E LEU* 3.9 15.5 - - - +
71E GLY* 5.5 2.9 - - - +
75E PHE* 3.7 28.3 - - + -
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Residues in contact with VAL 13 (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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9E LEU 3.5 15.7 - - - +
10E PHE* 3.3 22.9 - - - +
11E GLY 4.1 3.4 - - - +
12E MET* 1.3 87.0 - - + +
14E ASP* 1.3 62.8 + - - +
15E SER 3.3 25.7 + - - +
16E LYS* 4.4 1.3 - - - +
18E ARG* 4.1 9.0 - - + +
19E LEU* 3.7 32.1 - - + +
22E VAL* 5.6 1.3 - - + -
68E LEU* 6.3 1.1 - - + -
75E PHE* 3.9 24.5 - - + -
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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