Contacts of the helix formed by residues 4 - 21 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ALA 4.3 5.2 - - - +
3C LEU* 1.3 75.7 - - - +
5C ASN* 1.3 53.3 + - - +
6C ALA* 3.1 11.1 + - - +
7C GLN* 2.7 63.9 + - + +
8C ILE* 2.7 18.8 + - - +
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Residues in contact with ASN 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU 4.1 0.4 + - - -
4C THR* 1.3 72.6 - - - +
6C ALA* 1.3 63.9 + - - +
8C ILE* 3.2 9.2 + - - +
9C LEU* 3.1 42.1 + - - +
84C LEU* 4.4 21.4 - - + +
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Residues in contact with ALA 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C THR* 3.0 8.5 + - - +
5C ASN* 1.3 82.7 + - - +
7C GLN* 1.3 61.4 + - + +
9C LEU* 3.6 8.8 + - - +
10C ALA* 3.2 20.4 + - - +
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Residues in contact with GLN 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA 4.3 1.4 - - - +
3C LEU* 3.6 22.2 - - + +
4C THR* 2.7 57.3 + - + +
6C ALA* 1.3 71.1 - - + +
8C ILE* 1.3 66.0 + - - +
10C ALA* 3.0 22.1 - - - +
11C VAL* 3.2 11.7 + - - +
68C ILE* 3.3 32.6 - - + +
69C ASN* 4.1 15.4 + - - +
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Residues in contact with ILE 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.2 27.8 - - + +
4C THR 2.7 23.6 + - - +
5C ASN* 3.5 7.2 - - - +
7C GLN* 1.3 71.9 - - - +
9C LEU* 1.3 57.7 + - - +
11C VAL* 2.8 30.5 + - + +
12C ILE* 3.0 21.8 + - + -
75C TRP* 5.6 5.4 - - + +
83C LEU* 3.8 38.8 - - + +
84C LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASN* 3.1 33.7 + - - +
6C ALA* 3.9 7.9 - - - +
8C ILE* 1.3 79.2 - - - +
10C ALA* 1.3 60.7 + - - +
12C ILE* 3.4 5.1 + - - +
13C ASP* 2.6 38.0 + - - +
84C LEU* 4.1 11.9 - - + -
157D ARG* 2.5 51.6 - - - +
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA 3.2 11.5 + - - +
7C GLN* 3.0 18.3 + - - +
9C LEU* 1.3 80.5 - - - +
11C VAL* 1.3 60.5 + - + +
13C ASP* 3.6 6.1 - - - +
14C SER* 3.0 22.6 + - - -
68C ILE* 6.5 0.4 - - + -
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.6 4.0 - - + -
7C GLN 3.3 15.0 - - - +
8C ILE* 2.8 18.0 + - + +
10C ALA* 1.3 68.4 - - + +
12C ILE* 1.3 68.5 + - + +
14C SER* 2.4 28.7 + - - -
15C TRP* 2.8 7.2 + - - +
64C TYR* 3.9 18.8 - - + -
66C ARG* 4.2 6.3 - - + +
68C ILE* 4.1 24.5 - - + -
75C TRP* 3.7 36.8 - - + -
80C VAL* 4.5 8.7 - - + -
83C LEU* 5.0 4.3 - - + -
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.0 27.6 + - + +
9C LEU* 3.7 7.4 - - - +
11C VAL* 1.3 78.4 - - - +
13C ASP* 1.3 58.0 + - - +
15C TRP* 3.2 3.4 - - + +
16C GLU* 2.9 40.4 + - + +
80C VAL* 3.6 39.5 - - + +
81C PRO* 4.4 16.8 - - + +
83C LEU* 4.5 5.6 - - + +
84C LEU* 4.2 6.5 - - + -
157D ARG* 3.2 48.5 - - + +
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Residues in contact with ASP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 2.6 34.6 + - - +
10C ALA* 3.6 7.0 - - - +
11C VAL 2.8 1.2 + - - -
12C ILE* 1.3 72.6 - - - +
14C SER* 1.3 66.6 + - - +
16C GLU* 3.5 6.3 + - - +
17C GLU* 3.1 25.6 + - - +
157D ARG* 3.7 30.7 + - - +
158D GLY* 4.5 5.4 + - - -
160D HIS* 5.0 1.4 - - - -
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 3.0 10.0 + - - -
11C VAL* 2.4 41.2 + - - -
13C ASP* 1.3 73.5 - - - +
15C TRP* 1.3 61.3 + - - +
17C GLU* 3.3 11.5 - - - +
18C THR* 3.2 24.6 + - - -
64C TYR* 3.5 14.7 + - - -
66C ARG* 3.9 23.1 - - - -
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Residues in contact with TRP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL 2.8 8.9 + - - +
12C ILE* 3.2 11.7 - - + +
14C SER* 1.3 74.6 + - - +
16C GLU* 1.3 78.9 + - + +
17C GLU 2.8 4.5 + - - -
18C THR* 2.9 4.2 + - - -
19C VAL* 2.8 45.5 + - + +
54C PHE* 3.6 24.6 - + - -
64C TYR* 3.7 22.6 - + + -
77C SER 3.2 29.2 + - - -
78C HIS* 4.6 2.0 - - - -
80C VAL* 3.7 33.8 - - + +
81C PRO* 3.4 35.2 - - + -
106C HIS* 3.2 32.8 - + - -
108C PRO* 3.9 19.1 - - + -
111C LEU* 4.5 4.5 - - + -
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 2.9 26.3 + - + +
13C ASP* 3.8 6.9 - - - +
15C TRP* 1.3 92.8 - - + +
17C GLU* 1.3 57.2 + - - +
20C GLY* 2.8 24.2 + - - -
81C PRO* 6.1 0.7 - - + +
108C PRO* 4.7 2.4 - - + +
155D GLN 4.6 1.2 - - - +
156D GLN* 3.3 17.9 - - - +
157D ARG* 2.7 34.2 + - - +
158D GLY* 3.2 25.5 + - - -
159D SER 4.3 1.9 + - - -
160D HIS* 3.5 14.2 - - + +
161D PHE* 3.2 28.6 - - + -
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASP 3.1 13.6 + - - +
14C SER* 3.3 15.1 - - - +
15C TRP 2.8 0.6 + - - -
16C GLU* 1.3 74.8 - - - +
18C THR* 1.3 67.0 + - - +
20C GLY* 3.1 13.3 + - - -
21C GLN* 3.6 22.0 + - - +
160D HIS* 3.7 28.9 + - + +
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C SER 3.2 11.0 + - - -
15C TRP* 2.9 11.1 + - - -
17C GLU* 1.3 76.8 + - - +
19C VAL* 1.3 62.2 - - - +
21C GLN* 3.3 21.5 + - + +
22C PHE* 4.0 10.1 + - + -
51C GLY* 4.3 4.3 - - - -
52C VAL* 3.4 53.8 + - + +
54C PHE* 3.7 21.5 - - + -
64C TYR* 4.3 3.4 + - - -
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 2.8 39.6 + - + +
16C GLU* 4.3 0.2 - - - -
18C THR* 1.3 75.4 - - - +
20C GLY* 1.3 64.1 + - - +
21C GLN 3.0 1.6 + - - -
22C PHE* 3.0 32.5 + - + +
42C TYR* 3.9 6.2 - - + -
54C PHE* 3.6 26.5 - - + -
106C HIS* 3.6 29.8 - - + +
161D PHE* 3.3 28.3 - - + -
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Residues in contact with GLY 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU 2.8 20.1 + - - -
17C GLU 3.1 5.6 + - - -
19C VAL* 1.3 75.9 - - - +
21C GLN* 1.3 58.3 + - - +
22C PHE 3.3 2.6 + - - +
24C VAL* 5.2 1.0 - - - +
42C TYR* 3.8 16.5 - - - -
160D HIS* 4.4 13.0 - - - +
161D PHE* 3.6 15.0 - - - -
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.6 25.1 + - - +
18C THR* 3.3 12.0 + - - +
19C VAL 3.0 1.4 + - - -
20C GLY* 1.3 75.3 - - - +
22C PHE* 1.3 68.1 + - + +
23C PRO* 3.5 4.2 - - - +
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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) + - + + + + + -
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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