Contacts of the helix formed by residues 1 - 20 (chain D) 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 PHE 1 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D VAL* 1.3 61.8 + - - +
3D ASN* 3.3 5.6 - - + +
4D GLN* 3.1 32.2 + - + +
5D HIS* 3.0 24.1 + - - +
8G THR 5.3 9.0 - - - +
9G SER* 5.8 5.2 - - - +
10G ILE* 3.9 22.2 - - - +
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Residues in contact with VAL 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D PHE* 1.3 72.9 - - - +
3D ASN* 1.3 62.2 + - - +
5D HIS* 3.1 8.4 + - + +
6D LEU* 2.8 46.6 + - + +
6G CYS 3.7 7.4 - - - +
7G CYS* 3.4 31.6 - - - +
8G THR 3.8 2.8 + - - +
9G SER* 3.4 36.3 - - - +
10G ILE* 3.6 6.1 - - + +
309G CRS 4.4 13.7 - - + +
7H CYS* 4.6 4.7 - - + -
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Residues in contact with ASN 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D PHE* 3.3 4.8 + - + +
2D VAL* 1.3 78.0 - - - +
4D GLN* 1.3 67.9 + - + +
6D LEU* 3.3 14.1 + - - +
7D CYS* 2.9 30.0 + - - +
3H ASN* 5.8 4.2 - - - +
3L ASN* 4.6 16.7 + - - +
6L LEU* 4.9 2.9 - - - +
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Residues in contact with GLN 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.8 1.0 + - - -
3C VAL* 4.3 25.6 - - + +
7C CYS* 4.5 15.5 - - - +
1D PHE* 3.4 40.5 - - + +
3D ASN* 1.3 79.0 - - + +
5D HIS* 1.3 60.6 + - - +
7D CYS* 3.8 5.9 - - - +
8D GLY* 2.9 26.3 + - - -
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Residues in contact with HIS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 2.6 55.0 + + - -
17B LEU* 3.9 11.7 - - + +
20B GLY* 6.4 1.8 - - - -
1D PHE 3.0 12.1 + - - +
2D VAL* 3.3 14.4 - - + +
4D GLN* 1.3 80.2 - - - +
6D LEU* 1.3 66.6 + - + +
9D SER* 3.2 8.2 + - - -
10G ILE* 4.0 29.9 - - + +
309G CRS 3.6 47.8 - + + +
10H HIS* 6.0 0.7 - - + -
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D VAL* 2.8 35.6 + - + +
3D ASN* 3.6 12.8 - - - +
5D HIS* 1.3 75.0 - - + +
7D CYS* 1.3 67.4 + - - +
9D SER* 3.1 14.7 + - - -
10D HIS* 3.4 18.1 + - - -
304D CL 3.9 21.3 - - + -
309G CRS 4.3 15.5 - - + -
3H ASN 5.0 2.2 - - - +
6H LEU* 4.6 4.0 - - + -
7H CYS* 4.2 20.6 - - + +
10H HIS* 3.7 35.9 - - + -
6L LEU* 4.7 4.9 - - + -
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Residues in contact with CYS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C CYS* 2.0 56.5 - - + +
307C CRS 3.9 21.0 - - - -
3D ASN 2.9 17.2 + - - +
4D GLN* 3.8 2.5 - - - +
6D LEU* 1.3 75.7 - - - +
8D GLY* 1.3 56.8 + - - +
10D HIS* 3.0 6.2 + - - +
11D LEU* 2.9 25.8 + - - +
2L VAL* 4.2 6.5 - - + -
6L LEU* 4.1 20.1 - - + +
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Residues in contact with GLY 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.3 17.9 - - - -
3C VAL* 5.4 0.7 - - - -
7C CYS* 5.1 0.4 - - - -
4D GLN 2.9 14.6 + - - -
5D HIS 3.4 0.2 + - - -
6D LEU 3.2 0.2 - - - -
7D CYS* 1.3 78.4 - - - +
9D SER* 1.3 59.9 + - - +
11D LEU* 3.3 10.6 + - - +
12D VAL* 3.1 30.7 + - - +
26D TYR* 3.7 15.9 - - - -
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Residues in contact with SER 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 2.8 45.7 + - - +
16B TYR* 3.4 21.9 - - - -
17B LEU* 6.1 1.3 - - - -
5D HIS* 3.2 8.8 + - - -
6D LEU* 3.1 11.5 + - - -
8D GLY* 1.3 76.5 - - - +
10D HIS* 1.3 62.0 + - - +
12D VAL* 3.3 5.8 - - - +
13D GLU* 3.5 1.6 + - - +
10H HIS* 3.4 29.7 + - - -
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Residues in contact with HIS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C CRS 4.1 12.6 - - + +
6D LEU 3.4 17.9 + - - -
7D CYS 3.0 7.4 + - - +
9D SER* 1.3 76.2 - - - +
11D LEU* 1.3 66.9 + - - +
13D GLU* 3.2 8.1 + - - +
14D ALA* 3.0 22.3 + - - +
302D ZN 2.0 36.6 - - - -
304D CL 3.5 1.2 - - + +
10H HIS* 3.3 9.5 + + - -
17J LEU* 5.7 0.7 - - - +
5L HIS* 5.5 2.6 + - - +
6L LEU* 3.4 25.8 - - + +
9L SER* 3.3 34.7 + - - -
10L HIS* 3.6 9.2 - + - -
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 4.0 34.1 - - + +
3C VAL* 4.3 7.0 - - + -
6C CYS* 3.8 9.6 - - + -
7C CYS* 3.7 26.2 - - - -
16C LEU* 3.6 28.4 - - + +
307C CRS 3.5 30.7 - - + -
7D CYS* 2.9 12.5 + - - +
8D GLY* 3.3 14.3 + - - +
10D HIS* 1.3 77.5 - - - +
12D VAL* 1.3 58.5 + - - +
14D ALA* 3.2 3.5 + - - +
15D LEU* 2.9 32.7 + - - +
26D TYR* 4.7 4.9 - - + +
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Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.5 20.4 - - + +
13B GLU* 3.2 22.7 - - - +
16B TYR* 3.8 23.1 - - + -
24B PHE* 4.0 9.0 - - + -
8D GLY 3.1 14.6 + - - +
9D SER 3.3 8.5 - - - +
11D LEU* 1.3 76.4 - - - +
13D GLU* 1.3 65.3 + - - +
15D LEU* 3.4 7.3 + - - -
16D TYR* 3.0 22.3 + - - +
24D PHE* 3.6 7.6 - - + -
26D TYR* 3.7 35.0 - - + -
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 2.6 37.4 + - - +
12B VAL* 4.9 0.9 - - - -
13B GLU* 3.3 19.6 + - - +
9D SER 3.9 2.7 - - - +
10D HIS* 3.2 11.6 + - - +
11D LEU 3.2 0.6 - - - -
12D VAL* 1.3 80.6 - - - +
14D ALA* 1.3 64.8 + - - +
16D TYR* 3.2 12.1 + - - +
17D LEU* 3.1 44.3 + - + +
10J HIS* 5.7 1.9 + - - -
13J GLU* 6.0 6.1 - - + -
17J LEU* 5.1 4.9 - - + -
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Residues in contact with ALA 14 (chain D).
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* 5.9 0.4 - - + -
16C LEU* 3.8 14.4 - - + -
307C CRS 3.6 31.4 - - + -
10D HIS 3.0 10.7 + - - +
11D LEU* 3.6 8.3 - - - +
13D GLU* 1.3 78.1 - - - +
15D LEU* 1.3 51.4 + - - +
17D LEU* 3.2 4.0 + - - +
18D VAL* 2.8 41.2 + - + +
17J LEU* 4.0 19.7 - - + +
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.8 23.8 - - + -
16C LEU* 3.5 37.2 - - + +
19C TYR* 4.1 13.7 - - + -
11D LEU 2.9 19.9 + - - +
12D VAL* 3.7 5.4 - - - +
14D ALA* 1.3 73.1 - - - +
16D TYR* 1.3 60.5 + - - +
18D VAL* 4.3 2.0 - - + +
19D CYS* 2.7 50.1 + - - +
24D PHE* 3.6 37.2 - - + -
25D PHE 5.0 3.1 - - - +
26D TYR* 4.4 14.4 - - + -
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Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLN 3.8 1.0 + - - -
5B HIS* 2.6 61.5 + + - -
8B GLY* 3.2 12.6 - - - -
9B SER* 3.5 17.7 - - - -
12B VAL* 3.7 16.8 - - + -
26B TYR* 3.4 41.1 + + - -
12D VAL 3.0 14.5 + - - +
13D GLU* 3.2 28.7 - - - +
15D LEU* 1.3 80.4 - - - +
17D LEU* 1.3 63.3 + - + +
20D GLY* 3.3 19.2 + - - +
24D PHE* 3.6 10.3 - - + -
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Residues in contact with LEU 17 (chain D).
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* 3.3 35.6 - - + +
13D GLU* 3.1 29.2 + - + +
14D ALA 3.7 4.9 - - - +
16D TYR* 1.3 80.2 - - + +
18D VAL* 1.3 64.2 + - + +
20D GLY* 3.8 7.1 + - - -
13I LEU* 3.8 28.3 - - + +
310I CRS 3.7 14.1 - - + -
10J HIS 5.9 0.2 - - - +
13J GLU* 5.2 1.8 - - + -
14J ALA* 4.2 22.0 - - + +
17J LEU* 3.7 28.9 - - + -
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Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.8 39.7 - - + +
16C LEU* 4.6 8.1 - - + -
17C GLU* 3.8 44.1 - - + +
20C CYS* 4.2 3.3 - - - -
14D ALA* 2.8 26.8 + - - +
15D LEU* 4.1 4.3 - - - +
17D LEU* 1.3 75.9 - - + +
19D CYS* 1.3 61.1 + - - +
20D GLY* 4.7 0.2 - - - -
22D ARG* 5.8 0.3 - - - -
13I LEU* 4.0 16.9 - - + +
17J LEU* 6.5 0.2 - - + -
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Residues in contact with CYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C CYS* 2.0 54.7 - - + -
15D LEU* 2.7 37.5 + - - +
16D TYR 4.8 0.2 - - - +
18D VAL* 1.3 75.7 - - - +
20D GLY* 1.3 64.2 + - - +
21D GLU 3.2 0.5 + - - -
22D ARG* 3.0 25.7 + - - +
23D GLY* 3.4 24.5 - - - +
24D PHE* 3.9 11.2 - - + -
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Residues in contact with GLY 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 5.4 2.1 - - - -
28B PRO* 3.9 8.1 - - - +
16D TYR* 3.3 18.0 + - - +
17D LEU 3.8 5.3 + - - -
18D VAL 3.4 2.6 - - - -
19D CYS* 1.3 77.2 - - - +
21D GLU* 1.3 64.7 + - - -
22D ARG 3.1 1.7 + - - -
23D GLY* 3.1 12.3 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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