Contacts of the helix formed by residues 2 - 20 (chain J) in PDB entry 1EV6
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 VAL 2 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E CYS 3.9 7.6 - - - +
7E CYS 3.3 12.5 + - - +
9E SER* 3.7 7.9 - - - -
10E ILE* 3.6 38.6 - - + +
308E CRS 4.5 10.3 - - + +
7F CYS* 4.0 21.8 - - - -
1J PHE* 1.3 84.7 - - + +
3J ASN* 1.3 62.9 + - - +
4J GLN 3.4 2.9 - - - -
5J HIS* 3.2 13.1 + - + -
6J LEU* 3.1 31.5 + - + +
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Residues in contact with ASN 3 (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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6B LEU* 5.1 2.4 - - + +
1J PHE* 3.2 45.5 + - + +
2J VAL* 1.3 73.7 - - - +
4J GLN* 1.3 75.4 + - - +
6J LEU* 3.3 5.3 + - - +
7J CYS* 2.8 30.8 + - - +
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Residues in contact with GLN 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I VAL* 4.3 28.2 - - + +
4I GLU* 5.5 2.4 + - - +
7I CYS* 5.0 5.0 - - + -
1J PHE 5.2 0.2 + - - -
2J VAL 3.4 0.6 - - - -
3J ASN* 1.3 91.0 - - - +
5J HIS* 1.3 62.9 + - - +
7J CYS* 3.4 6.9 + - - +
8J GLY* 3.0 19.6 + - - -
26J TYR* 5.1 0.9 + - - -
16L TYR* 3.9 2.3 + - - -
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Residues in contact with HIS 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 3.6 30.4 - - + +
308E CRS 3.5 41.3 - + + -
10F HIS* 5.3 3.1 + - + +
2J VAL* 3.2 18.6 + - + +
4J GLN* 1.3 77.8 - - - +
6J LEU* 1.3 68.3 + - + +
8J GLY 3.3 0.2 + - - -
9J SER* 3.0 13.6 + - - -
16L TYR* 2.6 51.4 + + - -
17L LEU* 4.8 14.3 - - + +
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Residues in contact with LEU 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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6B LEU* 4.4 5.6 - - + -
303B CL 3.8 21.1 - - + -
308E CRS 3.8 21.5 - - + -
6F LEU* 4.5 4.0 - - + -
7F CYS* 4.3 14.8 - - - +
10F HIS* 3.5 33.7 - - + +
1J PHE* 3.7 34.3 - - + -
2J VAL* 3.1 13.6 + - + +
3J ASN* 3.6 6.5 - - - +
5J HIS* 1.3 83.6 - - + +
7J CYS* 1.3 63.5 + - - +
9J SER* 3.2 10.8 + - - -
10J HIS* 3.1 24.6 + - - -
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Residues in contact with CYS 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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2B VAL* 4.4 5.8 - - + -
6B LEU* 4.2 15.0 - - + +
7I CYS* 2.0 59.0 - - + +
310I CRS 4.0 15.0 - - - -
3J ASN 2.8 17.2 + - - +
4J GLN* 3.7 4.5 - - - +
5J HIS 3.3 0.2 - - - -
6J LEU* 1.3 77.5 - - - +
8J GLY* 1.3 57.3 + - - +
10J HIS* 3.0 6.4 + - - +
11J LEU* 2.8 35.3 + - - +
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Residues in contact with GLY 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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3I VAL* 5.5 0.2 - - - -
7I CYS* 4.6 0.8 - - - -
4J GLN 3.0 12.2 + - - -
7J CYS* 1.3 76.6 - - - +
9J SER* 1.3 63.0 + - - +
11J LEU* 3.7 7.7 - - - +
12J VAL* 3.0 29.3 + - - +
26J TYR* 3.3 26.2 - - - -
16L TYR* 3.5 13.5 - - - -
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Residues in contact with SER 9 (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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10F HIS* 3.3 31.7 + - - -
5J HIS* 3.0 16.9 + - - -
6J LEU* 3.3 11.0 - - - -
7J CYS 3.2 0.2 - - - -
8J GLY* 1.3 77.8 - - - +
10J HIS* 1.3 61.3 + - - +
12J VAL 3.6 0.3 + - - -
13J GLU* 3.5 5.0 + - - +
13L GLU* 2.5 46.0 + - - +
16L TYR* 3.4 17.6 - - - -
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Residues in contact with HIS 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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5B HIS* 5.7 1.4 - - + -
6B LEU* 3.3 30.8 - - + +
9B SER* 3.7 27.2 + - - -
10B HIS* 3.6 10.5 - + - -
301B ZN 2.0 38.1 - - - -
303B CL 3.4 1.3 - - + +
13D GLU* 5.7 2.2 + - - -
17D LEU* 5.9 0.2 - - - +
10F HIS* 3.2 9.6 + + - -
310I CRS 3.9 12.8 - - + +
6J LEU 3.1 22.2 + - - -
7J CYS 3.0 6.2 + - - +
9J SER* 1.3 74.3 - - - +
11J LEU* 1.3 67.0 + - - +
13J GLU* 3.3 7.5 + - - +
14J ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 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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2I ILE* 3.9 44.4 - - + +
3I VAL* 4.5 1.6 - - - -
6I CYS* 3.8 12.8 - - + -
7I CYS* 3.7 26.5 - - - -
16I LEU* 4.1 8.3 - - + -
310I CRS 3.5 37.9 - - + -
7J CYS* 2.8 15.6 + - - +
8J GLY* 3.1 13.4 + - - +
10J HIS* 1.3 77.7 - - - +
12J VAL* 1.3 59.0 + - - +
14J ALA* 3.1 4.1 + - - +
15J LEU* 2.8 35.4 + - - +
26J TYR* 4.4 6.5 - - + +
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Residues in contact with VAL 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J GLY 3.0 18.4 + - - +
9J SER 3.8 4.5 - - - +
11J LEU* 1.3 77.8 - - - +
13J GLU* 1.3 57.6 + - - +
15J LEU* 3.5 5.5 + - - +
16J TYR* 3.1 26.2 + - - +
24J PHE* 3.7 7.5 - - + -
26J TYR* 3.7 32.3 - - + -
12L VAL* 3.7 37.7 - - + +
13L GLU* 3.6 11.9 - - - +
16L TYR* 3.8 15.7 - - + -
24L PHE* 3.9 11.4 - - + -
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Residues in contact with GLU 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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13D GLU* 6.0 6.5 - - + -
17D LEU* 5.2 2.2 - - + -
9J SER 3.5 2.9 + - - +
10J HIS* 3.3 10.6 + - - +
11J LEU 3.3 0.2 - - - -
12J VAL* 1.3 77.0 - - - +
14J ALA* 1.3 63.7 + - - +
16J TYR* 3.4 7.1 + - - +
17J LEU* 3.2 29.3 + - + +
9L SER* 2.4 51.6 + - - +
12L VAL* 2.9 11.8 - - - +
13L GLU* 2.7 37.1 - - + +
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Residues in contact with ALA 14 (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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17D LEU* 4.2 19.0 - - + +
13I LEU* 5.1 2.0 - - + -
16I LEU* 4.0 14.1 - - + -
310I CRS 3.5 32.1 - - + -
10J HIS 3.0 10.0 + - - +
11J LEU* 3.6 7.9 - - - +
13J GLU* 1.3 75.0 - - - +
15J LEU* 1.3 60.2 + - - +
17J LEU* 3.2 2.4 + - - +
18J VAL* 2.8 35.4 + - - +
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Residues in contact with LEU 15 (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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2I ILE* 3.8 24.2 - - + -
16I LEU* 3.4 39.9 - - + +
19I TYR* 3.8 13.0 - - + -
11J LEU 2.8 20.0 + - - +
12J VAL* 3.8 3.4 - - - +
14J ALA* 1.3 76.3 - - - +
16J TYR* 1.3 56.7 + - - +
18J VAL* 4.5 1.6 - - + +
19J CYS* 2.8 44.2 + - - +
24J PHE* 3.6 36.8 - - + -
25J PHE 4.0 13.2 - - - +
26J TYR* 4.5 10.3 - - + -
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Residues in contact with TYR 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 VAL 3.1 14.6 + - - +
13J GLU* 3.5 11.9 - - - +
15J LEU* 1.3 79.7 - - - +
17J LEU* 1.3 71.3 + - + +
19J CYS* 4.8 0.3 - - - +
20J GLY* 3.5 20.5 + - - +
24J PHE* 3.5 11.6 - - + -
4L GLN 3.8 0.9 + - - -
5L HIS* 2.6 55.2 + + - -
8L GLY* 3.3 17.1 - - - -
9L SER* 3.3 29.2 - - - -
12L VAL* 3.8 19.3 - - + -
26L TYR* 3.6 36.4 + + - -
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Residues in contact with LEU 17 (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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13C LEU* 3.8 26.1 - - + +
307C CRS 3.7 26.7 - - + -
10D HIS 5.7 0.7 - - - +
13D GLU* 5.1 5.4 - - + -
14D ALA* 4.0 23.1 - - + +
17D LEU* 3.7 28.7 - - + -
18D VAL* 6.5 0.7 - - + -
13J GLU* 3.2 12.3 + - + +
14J ALA* 3.2 6.7 + - - +
15J LEU 3.2 0.4 - - - -
16J TYR* 1.3 85.2 - - + +
18J VAL* 1.3 67.2 + - + +
20J GLY* 3.7 6.6 + - - -
5L HIS* 3.8 19.7 - - + +
9L SER* 6.3 0.7 - - - -
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Residues in contact with VAL 18 (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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13C LEU* 4.1 18.2 - - + +
13I LEU* 3.7 46.7 - - + +
16I LEU* 4.5 6.5 - - + -
17I GLU* 3.3 43.2 - - + +
20I CYS* 4.1 2.9 - - - -
14J ALA* 2.8 24.3 + - - +
15J LEU* 4.0 4.0 - - - +
17J LEU* 1.3 75.3 - - + +
19J CYS* 1.3 64.0 + - - +
20J GLY* 3.5 0.7 + - - -
22J ARG* 3.6 10.9 + - - -
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Residues in contact with CYS 19 (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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19I TYR 4.3 1.3 - - - -
20I CYS* 2.0 56.3 - - + -
15J LEU* 2.8 34.2 + - - +
16J TYR 4.8 0.4 - - - +
18J VAL* 1.3 74.1 - - - +
20J GLY* 1.3 63.6 - - - +
22J ARG* 3.1 30.1 + - - +
23J GLY* 3.2 22.4 - - - +
24J PHE* 3.8 11.0 - - + -
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Residues in contact with GLY 20 (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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16J TYR* 3.5 17.9 + - - +
17J LEU 3.7 5.2 + - - -
18J VAL 3.4 4.0 + - - -
19J CYS* 1.3 77.0 - - - +
21J GLU* 1.3 66.9 + - - +
23J GLY* 3.2 13.7 + - - -
26L TYR* 5.1 3.8 - - - -
28L PRO* 3.9 5.0 - - - +
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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
------------------------------------------------------------
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