Contacts of the helix formed by residues 4 - 21 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA 4.3 5.4 - - - +
3A LEU* 1.3 76.8 - - - +
5A ASN* 1.3 57.8 + - - +
6A ALA* 3.3 10.9 + - - +
7A GLN* 2.7 61.9 + - + +
8A ILE* 2.8 14.4 + - - +
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Residues in contact with ASN 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU 4.0 1.0 + - - -
4A THR* 1.3 71.8 - - - +
6A ALA* 1.3 64.9 + - - +
8A ILE* 3.1 11.2 + - - +
9A LEU* 3.0 43.0 + - - +
84A LEU* 4.1 23.0 - - - +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 3.3 8.2 + - - +
5A ASN* 1.3 81.3 + - - +
7A GLN* 1.3 62.9 + - + +
9A LEU* 3.6 9.0 + - - +
10A ALA* 3.2 20.8 + - - +
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA 4.2 1.4 - - - +
3A LEU* 3.6 20.2 - - + +
4A THR* 2.7 64.4 + - + +
6A ALA* 1.3 70.0 - - + +
8A ILE* 1.3 64.2 + - - +
10A ALA* 3.0 22.1 - - - +
11A VAL* 3.2 11.7 - - - +
68A ILE* 3.2 35.7 - - + +
69A ASN* 4.3 14.1 + - - +
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.2 26.5 - - + +
4A THR 2.8 22.7 + - - +
5A ASN* 3.3 8.1 - - - +
7A GLN* 1.3 71.5 - - - +
9A LEU* 1.3 59.9 + - - +
11A VAL* 2.6 38.8 + - + +
12A ILE* 3.0 14.4 + - + -
75A TRP* 5.5 4.3 - - + +
83A LEU* 3.9 38.4 - - + +
84A LEU* 3.6 28.9 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.0 41.5 + - - +
6A ALA* 3.8 8.1 - - - +
8A ILE* 1.3 80.4 - - - +
10A ALA* 1.3 62.8 + - - +
12A ILE* 3.2 9.4 + - + +
13A ASP* 2.8 31.4 + - - +
84A LEU* 3.7 23.8 - - + -
157B ARG* 3.5 38.6 - - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 3.2 11.7 + - - +
7A GLN* 3.0 19.7 - - - +
9A LEU* 1.3 80.0 - - - +
11A VAL* 1.3 61.2 + - + +
13A ASP* 3.3 6.8 + - - +
14A SER* 3.0 23.3 + - - -
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.6 4.5 - - + -
7A GLN 3.2 16.6 - - - +
8A ILE* 2.6 20.8 + - + +
10A ALA* 1.3 68.6 - - + +
12A ILE* 1.3 70.9 + - + +
14A SER* 2.5 23.2 + - - -
15A TRP* 2.8 9.4 + - - +
64A TYR* 4.0 18.6 - - + -
66A ARG* 4.2 6.3 - - + +
68A ILE* 4.5 15.7 - - + -
75A TRP* 3.9 38.1 - - + -
80A VAL* 4.5 8.7 - - + -
83A LEU* 4.9 4.7 - - + -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.0 28.4 + - + +
9A LEU* 3.6 12.6 - - + +
11A VAL* 1.3 79.3 - - - +
13A ASP* 1.3 59.5 + - - +
15A TRP* 3.0 4.2 - - + +
16A GLU* 2.8 36.0 + - + +
80A VAL* 3.5 41.1 - - + +
81A PRO* 4.4 16.4 - - + +
83A LEU* 4.4 5.6 - - + +
84A LEU* 4.4 15.0 - - + -
157B ARG* 3.8 33.2 - - + +
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 2.8 19.3 + - - +
10A ALA* 3.6 6.3 - - - +
12A ILE* 1.3 73.4 - - - +
14A SER* 1.3 66.5 + - - +
16A GLU* 3.4 7.4 + - - +
17A GLU* 3.1 25.1 + - - +
157B ARG* 2.6 50.0 + - - +
158B GLY* 4.9 2.9 + - - -
160B HIS* 5.8 0.3 - - - -
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Residues in contact with SER 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 3.0 14.0 + - - -
11A VAL* 2.5 25.8 + - - -
13A ASP* 1.3 75.3 - - - +
15A TRP* 1.3 59.6 + - - +
17A GLU* 3.3 12.6 - - - +
18A THR* 3.2 27.7 + - - -
64A TYR* 3.6 13.6 + - - -
66A ARG* 4.0 22.4 - - - -
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Residues in contact with TRP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL 2.8 11.2 + - - +
12A ILE* 3.0 12.3 - - + +
14A SER* 1.3 74.1 + - - +
16A GLU* 1.3 80.0 + - + +
17A GLU 3.0 2.0 + - - -
18A THR* 3.0 3.9 + - - -
19A VAL* 2.8 49.0 + - + +
54A PHE* 3.4 25.8 - + - -
64A TYR* 3.6 20.4 + + + -
77A SER 3.2 28.3 + - - -
78A HIS* 4.5 2.0 - - - -
80A VAL* 3.6 31.9 - - + +
81A PRO* 3.3 36.1 - - + -
106A HIS* 3.2 29.8 - + - -
108A PRO* 4.0 22.7 - - + -
111A LEU* 4.5 4.3 - - + -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 2.8 24.2 + - + +
13A ASP* 3.8 8.3 - - - +
15A TRP* 1.3 90.5 - - + +
17A GLU* 1.3 53.4 + - - +
19A VAL* 4.3 2.9 - - - -
20A GLY* 2.8 28.1 + - - -
108A PRO* 4.7 2.3 - - + +
155B GLN 4.5 1.6 - - - +
156B GLN* 3.4 16.1 - - - +
157B ARG* 2.7 40.7 + - - +
158B GLY* 3.1 25.5 + - - -
159B SER 4.9 0.3 + - - -
160B HIS* 4.1 13.0 - - + -
161B PHE* 3.4 21.6 - - + -
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASP 3.1 12.9 + - - +
14A SER* 3.3 17.1 - - - +
16A GLU* 1.3 74.5 - - - +
18A THR* 1.3 69.1 + - - +
20A GLY* 3.1 11.3 + - - -
21A GLN* 3.6 25.8 + - - +
160B HIS* 4.1 28.8 - - + +
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER 3.2 13.3 + - - -
15A TRP 3.0 4.2 + - - -
17A GLU* 1.3 82.1 + - - +
19A VAL* 1.3 61.3 + - - +
21A GLN* 3.4 18.1 + - - +
22A PHE* 4.0 11.0 - - + -
51A GLY* 4.3 4.9 - - - -
52A VAL* 3.4 54.6 + - + +
54A PHE* 3.8 19.3 - - + -
64A TYR* 4.3 4.1 + - - -
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 2.8 51.2 + - + +
16A GLU* 3.8 4.9 - - - +
18A THR* 1.3 77.6 - - - +
20A GLY* 1.3 57.6 + - - +
21A GLN 2.9 6.6 + - - -
22A PHE* 3.0 33.8 + - + +
42A TYR* 4.0 5.1 - - + -
54A PHE* 3.8 16.4 - - + -
106A HIS* 3.5 32.8 - - + +
161B PHE* 3.5 21.1 - - + -
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Residues in contact with GLY 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU 2.8 18.8 + - - -
17A GLU 3.1 5.2 + - - -
19A VAL* 1.3 76.3 - - - +
21A GLN* 1.3 60.0 + - - +
22A PHE 3.3 2.8 + - - +
24A VAL* 5.2 1.2 - - - +
42A TYR* 3.8 14.9 - - - -
160B HIS* 4.4 14.7 - - - +
161B PHE* 3.5 16.8 - - - -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.6 26.0 + - - +
18A THR* 3.4 9.0 + - - +
19A VAL 2.9 1.8 + - - -
20A GLY* 1.3 76.5 - - - +
22A PHE* 1.3 67.4 - - - +
23A PRO* 3.6 4.5 - - - +
160B HIS* 6.3 1.4 - - - -
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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