Contacts of the helix formed by residues 4 - 20 (chain D) in PDB entry 1EVW
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 THR 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ALA 4.3 5.6 - - - +
3D LEU* 1.3 75.7 - - - +
5D ASN* 1.3 66.4 + - - +
6D ALA* 3.4 10.5 + - - +
7D GLN* 2.6 52.4 + - - +
8D ILE* 2.7 14.8 + - - +
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Residues in contact with ASN 5 (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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4D THR* 1.3 71.5 - - - +
6D ALA* 1.3 57.4 + - - +
8D ILE* 2.8 11.4 + - - +
9D LEU* 2.8 51.9 + - + +
84D LEU* 4.4 22.0 - - - +
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Residues in contact with ALA 6 (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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4D THR* 3.4 8.5 + - - +
5D ASN* 1.3 80.8 - - - +
7D GLN* 1.3 63.4 + - + +
9D LEU* 3.7 9.9 + - - +
10D ALA* 3.2 21.0 + - - +
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Residues in contact with GLN 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA 4.3 1.4 - - - +
3D LEU* 3.7 21.3 - - + +
4D THR* 2.6 64.9 + - + +
6D ALA* 1.3 70.5 - - + +
8D ILE* 1.3 64.7 - - - +
10D ALA* 3.2 14.4 - - - +
11D VAL* 3.2 17.5 - - - +
68D ILE* 3.3 33.5 - - + +
69D ASN* 4.3 13.8 + - - +
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Residues in contact with ILE 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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3D LEU* 4.2 27.6 - - + +
4D THR 2.7 22.8 + - - +
5D ASN* 2.8 8.7 + - - +
7D GLN* 1.3 70.5 - - - +
9D LEU* 1.3 54.6 + - - +
11D VAL* 2.6 33.1 + - + +
12D ILE* 3.1 15.1 + - + -
75D TRP* 5.6 4.7 - - + +
83D LEU* 3.9 36.6 - - + +
84D LEU* 3.5 36.6 - - + -
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Residues in contact with LEU 9 (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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157C ARG* 2.9 46.7 - - - +
5D ASN* 2.8 41.7 + - + +
6D ALA* 3.9 7.9 - - - +
8D ILE* 1.3 74.6 - - - +
10D ALA* 1.3 60.1 + - - +
12D ILE* 3.3 7.4 + - + +
13D ASP* 2.7 34.3 + - - +
84D LEU* 4.2 20.2 - - + -
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Residues in contact with ALA 10 (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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6D ALA 3.2 13.2 + - - +
7D GLN* 3.2 15.3 - - - +
8D ILE 3.0 0.6 - - - -
9D LEU* 1.3 77.6 - - - +
11D VAL* 1.3 64.2 + - + +
13D ASP* 3.4 7.7 + - - +
14D SER* 3.0 23.5 + - - -
68D ILE* 6.5 0.2 - - + -
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Residues in contact with VAL 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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3D LEU* 4.5 4.3 - - + -
7D GLN 3.2 17.9 - - - +
8D ILE* 2.6 17.6 + - + +
10D ALA* 1.3 68.1 - - + +
12D ILE* 1.3 71.1 + - + +
14D SER* 2.4 25.6 + - - -
15D TRP* 2.8 7.1 + - - +
64D TYR* 3.9 24.2 - - + -
66D ARG* 4.2 6.5 - - + +
68D ILE* 4.3 22.2 - - + -
75D TRP* 3.9 30.5 - - + -
80D VAL* 4.7 7.4 - - + -
83D LEU* 5.0 5.4 - - + -
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Residues in contact with ILE 12 (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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157C ARG* 3.7 38.4 - - + +
8D ILE* 3.1 24.3 + - + +
9D LEU* 3.6 11.7 - - - +
11D VAL* 1.3 78.1 - - - +
13D ASP* 1.3 60.0 + - - +
15D TRP* 3.1 4.4 - - + +
16D GLU* 2.8 36.9 + - + +
80D VAL* 3.7 39.7 - - + +
81D PRO* 4.3 16.4 - - + +
83D LEU* 4.5 7.0 - - + +
84D LEU* 4.5 13.9 - - + -
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Residues in contact with ASP 13 (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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157C ARG* 3.0 39.9 + - - +
158C GLY* 4.9 3.8 + - - -
160C HIS* 5.5 0.9 + - - -
9D LEU* 2.7 26.0 + - - +
10D ALA* 3.6 6.3 + - - +
12D ILE* 1.3 74.9 - - - +
14D SER* 1.3 65.5 + - - +
16D GLU* 3.5 8.6 + - - +
17D GLU* 3.1 25.0 + - - +
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Residues in contact with SER 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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10D ALA 3.0 11.2 + - - -
11D VAL* 2.4 37.6 + - - -
13D ASP* 1.3 73.4 - - - +
15D TRP* 1.3 62.7 + - - +
17D GLU* 3.3 11.5 - - - +
18D THR* 3.2 25.1 + - - -
64D TYR* 3.2 15.3 + - - -
66D ARG* 3.9 22.8 - - - -
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Residues in contact with TRP 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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11D VAL 2.8 9.8 + - - +
12D ILE* 3.1 12.3 - - + +
14D SER* 1.3 73.2 + - - +
16D GLU* 1.3 88.1 + - + +
17D GLU 2.8 5.0 + - - -
18D THR* 2.9 4.7 + - - -
19D VAL* 2.8 36.8 + - + +
54D PHE* 3.6 24.2 - + - -
64D TYR* 3.6 21.3 - + + -
77D SER 3.1 30.1 + - - -
78D HIS* 4.6 2.9 - - - -
80D VAL* 3.5 33.9 - - + +
81D PRO* 3.3 35.2 - - + -
106D HIS* 3.3 26.5 - - + -
108D PRO* 4.0 23.6 - - + -
111D LEU* 4.6 4.5 - - + -
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Residues in contact with GLU 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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155C GLN 4.7 1.0 - - - +
156C GLN* 3.5 15.0 - - - +
157C ARG* 2.6 39.2 + - - +
158C GLY* 2.8 29.2 + - - -
159C SER 4.6 0.2 + - - -
160C HIS* 3.8 14.7 - - + -
161C PHE* 3.4 23.8 - - + -
12D ILE* 2.8 26.6 + - + +
13D ASP* 3.8 8.2 - - - +
15D TRP* 1.3 91.0 - - + +
17D GLU* 1.3 56.9 + - - +
20D GLY* 2.8 24.0 + - - -
108D PRO* 4.8 1.9 - - + +
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Residues in contact with GLU 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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160C HIS* 4.0 26.4 + - + +
13D ASP 3.1 13.8 + - - +
14D SER* 3.3 15.0 - - - +
15D TRP 2.8 0.8 + - - -
16D GLU* 1.3 75.2 - - - +
18D THR* 1.3 68.0 + - - +
20D GLY* 3.2 10.9 + - - -
21D GLN* 3.3 21.5 - - - +
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Residues in contact with THR 18 (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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14D SER 3.2 11.2 + - - -
15D TRP* 2.9 9.5 + - - -
17D GLU* 1.3 76.6 + - - +
19D VAL* 1.3 62.3 + - - +
21D GLN* 3.3 19.0 + - - +
22D PHE* 4.0 10.1 + - + -
51D GLY* 4.3 4.7 - - - -
52D VAL* 3.4 55.0 + - + +
54D PHE* 4.0 17.9 - - + -
64D TYR* 4.4 3.4 + - - -
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Residues in contact with VAL 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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161C PHE* 3.2 28.3 - - + -
15D TRP* 2.8 39.0 + - + +
16D GLU* 4.2 0.7 - - - -
18D THR* 1.3 74.1 - - - +
20D GLY* 1.3 59.0 + - - +
21D GLN 3.0 1.3 - - - -
22D PHE* 2.9 41.5 + - + +
42D TYR* 3.9 5.6 - - + -
54D PHE* 3.6 26.9 - - + -
106D HIS* 3.5 31.4 - - + +
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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
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160C HIS* 4.1 16.2 - - - +
161C PHE* 3.5 15.7 - - - -
16D GLU 2.8 19.6 + - - -
17D GLU 3.2 5.3 + - - -
19D VAL* 1.3 77.1 - - - +
21D GLN* 1.3 57.8 + - - +
22D PHE 3.4 2.1 + - - +
24D VAL* 5.3 1.0 - - - +
42D TYR* 3.9 14.4 - - - -
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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