Contacts of the helix formed by residues 3 - 16 (chain J) in PDB entry 2EHO
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 CYS 3 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1J MSE 2.7 6.7 - - - -
2J PHE* 1.3 82.4 - - - +
4J GLU* 1.3 63.9 + - - +
5J LYS 3.1 4.3 + - - -
6J ALA* 3.2 14.7 + - + +
7J MSE 3.3 13.0 + - - +
35J GLU* 4.1 8.5 - - - -
68J SER* 3.4 39.0 - - - -
71J ARG* 3.6 29.8 - - + +
72J ASN* 3.5 26.5 - - - +
71L TRP* 3.9 4.5 - - - -
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Residues in contact with GLU 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J MSE 3.6 13.8 + - - +
2J PHE* 2.9 25.1 + - + +
3J CYS* 1.3 76.4 - - - +
5J LYS* 1.3 62.9 + - - +
7J MSE 3.2 18.7 + - - +
8J GLU* 3.4 10.7 + - - +
11J ARG* 3.7 13.9 + - - -
35J GLU* 4.7 1.0 + - - -
29L HIS* 3.0 35.0 + - - -
31L LYS* 4.9 1.9 + - - -
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Residues in contact with LYS 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J CYS 3.1 0.8 - - - -
4J GLU* 1.3 74.6 - - - +
6J ALA* 1.3 67.1 + - - +
7J MSE 3.0 1.6 - - - -
8J GLU* 2.9 57.3 + - - +
9J LEU* 3.5 4.2 + - - +
25J ASN* 6.0 0.2 - - - +
28J GLY* 4.3 13.9 - - - +
31J GLN* 3.2 48.0 + - + +
32J VAL* 4.2 17.7 - - + +
35J GLU* 3.5 21.4 + - + +
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Residues in contact with ALA 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J CYS* 3.2 7.3 + - + +
5J LYS* 1.3 78.6 - - - +
7J MSE 1.3 57.9 + - - +
9J LEU* 3.0 27.8 - - + +
10J ILE* 3.2 10.9 + - - +
32J VAL* 4.0 21.3 - - + +
72J ASN* 3.5 23.6 + - - +
75J CYS* 3.6 30.3 - - + -
76J THR* 5.0 1.6 - - + -
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Residues in contact with MSE 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J CYS 3.3 10.5 + - - +
4J GLU 3.2 11.4 + - - +
5J LYS 3.0 0.6 - - - -
6J ALA* 1.3 75.7 - - - +
8J GLU* 1.3 65.0 + - - +
10J ILE* 3.0 5.5 + - + +
11J ARG* 2.8 53.3 + - - +
71J ARG* 3.7 26.5 - - - +
75J CYS* 4.5 1.3 - - - -
25L ILE* 3.8 18.2 - - - -
26L LEU* 3.3 35.7 - - + +
29L HIS* 3.4 43.7 - - + +
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Residues in contact with GLU 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J GLU 3.4 8.2 + - - +
5J LYS* 2.9 50.4 + - + +
7J MSE 1.3 78.6 - - - +
9J LEU* 1.3 64.8 + - + +
11J ARG* 3.4 18.1 + - - +
12J GLU* 3.2 25.8 + - - +
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Residues in contact with LEU 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LYS 3.5 3.0 + - - +
6J ALA* 3.0 17.7 + - - +
8J GLU* 1.3 82.6 - - + +
10J ILE* 1.3 59.4 + - + +
12J GLU* 4.0 4.2 + - - +
13J LEU* 3.9 10.6 + - - +
25J ASN* 3.1 41.1 - - - +
28J GLY* 4.4 3.8 - - - -
29J LEU* 4.3 17.9 - - + +
32J VAL* 4.3 21.1 - - + -
75J CYS 5.2 0.2 - - - +
76J THR* 4.5 18.4 - - + +
79J TYR* 3.2 59.6 - - + -
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Residues in contact with ILE 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ALA 3.2 11.8 + - - +
7J MSE 3.0 11.0 + - + +
9J LEU* 1.3 82.6 - - + +
11J ARG* 1.3 66.7 + - - +
13J LEU* 3.4 6.2 + - - +
14J HIS* 3.1 19.4 + - - +
75J CYS* 3.1 36.8 - - + +
78J ALA* 4.7 2.0 - - + -
79J TYR* 4.0 14.4 - - + +
22L LEU* 4.3 15.8 - - + +
25L ILE* 4.0 35.2 - - + -
26L LEU* 3.4 33.9 - - + -
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Residues in contact with ARG 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J GLU* 3.7 18.8 + - - -
7J MSE 2.8 48.4 + - + +
8J GLU* 3.7 32.7 - - - +
10J ILE* 1.3 72.8 - - - +
12J GLU* 1.3 54.6 + - - +
14J HIS* 3.1 8.0 + - + +
15J ARG* 2.7 67.7 + - - +
26L LEU* 3.9 17.2 - - + +
29L HIS* 4.1 11.9 + - - -
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Residues in contact with GLU 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J GLU 3.2 15.7 + - - +
9J LEU* 4.1 3.4 - - - +
10J ILE 3.3 0.2 - - - -
11J ARG* 1.3 77.8 - - - +
13J LEU* 1.3 58.6 + - - +
15J ARG* 3.7 12.1 - - - +
16J ALA* 2.9 29.3 + - + +
22J PRO* 3.9 29.2 - - + +
23J ALA 4.4 8.2 + - - +
25J ASN* 4.2 19.7 - - - +
79J TYR* 4.4 12.8 + - - -
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Residues in contact with LEU 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J LEU 3.9 2.8 + - - +
10J ILE* 3.4 5.5 + - - +
11J ARG 3.2 0.4 - - - -
12J GLU* 1.3 80.1 - - - +
14J HIS* 1.3 67.3 + - - +
16J ALA* 3.2 13.5 + - - +
22J PRO* 4.0 28.5 - - + -
79J TYR* 3.3 63.3 - - + +
82J ASP* 3.3 23.8 - - + +
83J ARG* 4.3 10.8 - - + +
86J ARG* 3.0 24.5 + - - +
7L ARG* 4.6 1.6 + - - -
22L LEU* 3.7 15.0 - - + -
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Residues in contact with HIS 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ILE 3.1 15.0 + - - +
11J ARG* 3.5 7.2 - - + +
13J LEU* 1.3 82.3 - - - +
15J ARG* 1.3 70.4 + - + +
16J ALA 3.4 4.7 + - - +
7L ARG* 3.5 27.6 + - - +
22L LEU* 3.9 8.2 - - + +
23L ASP* 3.7 21.5 + - - -
26L LEU* 3.4 33.1 - - + +
115L HIS* 6.4 0.9 - + - -
170L GLU* 4.6 21.0 + - + +
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Residues in contact with ARG 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ARG* 2.7 63.5 + - - +
12J GLU* 3.7 8.7 - - - +
14J HIS* 1.3 80.4 - - + +
16J ALA* 1.3 64.1 + - - +
17J PRO* 3.8 1.7 - - - +
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Residues in contact with ALA 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLU* 2.9 18.4 + - + +
13J LEU* 3.2 16.8 + - - +
14J HIS 4.0 5.5 - - - +
15J ARG* 1.3 82.4 - - - +
17J PRO* 1.3 76.5 - - + +
18J GLU* 3.2 4.3 + - - -
20J GLN 4.7 0.7 - - - +
22J PRO* 4.7 16.6 - - + -
86J ARG* 4.1 16.1 + - - +
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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