Contacts of the helix formed by residues 3 - 20 (chain A) in PDB entry 4EVI
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 ALA 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.0 0.2 + - - -
2A ASP* 1.3 74.8 - - - +
4A ALA* 1.3 58.1 + - - +
6A ALA* 3.1 9.4 + - - +
7A VAL* 2.9 33.7 + - + +
188B ARG* 4.9 3.6 - - - +
192B SER* 3.1 37.5 - - - +
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Residues in contact with ALA 4 (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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2A ASP* 3.3 9.5 + - - +
3A ALA* 1.3 78.7 - - - +
5A THR* 1.3 57.5 + - - +
7A VAL* 3.5 6.8 + - - +
8A GLU* 3.0 30.0 + - - +
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Residues in contact with THR 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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1A MET* 3.7 19.7 - - + -
2A ASP* 2.8 28.4 + - - -
4A ALA* 1.3 72.9 - - - +
6A ALA* 1.3 67.0 + - - +
8A GLU* 3.3 10.3 + - - +
9A LEU* 3.0 40.1 + - + +
105B ARG* 4.2 14.4 - - - +
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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
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1A MET* 3.7 21.2 - - + -
2A ASP 3.1 10.5 + - - +
3A ALA* 3.1 11.7 + - - +
5A THR* 1.3 76.3 - - - +
7A VAL* 1.3 56.2 + - - +
9A LEU 3.4 0.5 + - - -
10A LEU* 2.9 30.0 + - - +
185B LEU* 3.8 13.7 - - + +
188B ARG* 3.9 28.9 - - + -
189B ALA* 4.4 8.5 - - - +
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Residues in contact with VAL 7 (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 ALA 2.9 23.9 + - - +
4A ALA* 3.9 6.7 - - - +
6A ALA* 1.3 71.5 - - - +
8A GLU* 1.3 58.3 + - - +
10A LEU* 3.2 7.4 + - - +
11A ASP* 2.9 44.6 + - - +
189B ALA* 3.9 22.7 - - + +
192B SER* 5.2 5.2 - - - +
193B LYS* 3.8 40.2 - - + +
357B VAL 4.4 5.2 - - - +
358B GLY* 5.6 0.2 - - - -
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Residues in contact with GLU 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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4A ALA 3.0 19.1 + - - +
5A THR* 3.6 9.0 + - - +
7A VAL* 1.3 77.8 - - - +
9A LEU* 1.3 57.5 + - - +
11A ASP* 3.4 7.1 + - - +
12A ALA* 3.1 27.3 + - + +
102B PRO* 5.3 1.0 - - - +
105B ARG* 2.7 38.5 + - - +
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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
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1A MET* 3.7 20.9 - - + -
5A THR* 3.0 28.1 + - + +
8A GLU* 1.3 72.6 - - - +
10A LEU* 1.3 66.7 + - - +
12A ALA* 3.1 5.7 + - + +
13A GLN* 3.0 23.9 + - - +
102B PRO 5.0 0.9 - - - +
105B ARG* 3.4 50.0 - - + +
106B LEU* 4.2 21.0 - - + +
113B TYR* 3.6 28.9 - - + +
185B LEU* 3.8 22.1 - - + +
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Residues in contact with LEU 10 (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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6A ALA 2.9 17.9 + - - +
7A VAL* 3.2 6.5 + - - +
9A LEU* 1.3 76.0 - - - +
11A ASP* 1.3 61.0 + - - +
13A GLN* 3.5 16.7 - - - +
14A PRO* 3.3 15.6 - - - +
185B LEU* 4.0 10.4 - - + +
186B PHE* 3.7 34.5 - - + +
189B ALA* 3.6 26.7 - - + -
357B VAL* 4.0 2.0 - - + +
358B GLY* 3.5 27.6 - - - +
359B GLY* 3.3 11.1 - - - +
361B ARG* 3.5 26.2 - - - +
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Residues in contact with ASP 11 (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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7A VAL* 2.9 33.4 + - - +
8A GLU* 3.9 6.4 - - - +
9A LEU 3.2 0.2 - - - -
10A LEU* 1.3 76.4 - - - +
12A ALA* 1.3 55.8 + - - +
14A PRO* 3.3 14.0 - - - +
15A GLN* 4.4 7.7 + - - +
357B VAL 5.0 0.2 - - - +
358B GLY* 3.0 11.4 - - - -
359B GLY 2.7 31.0 + - - +
403B GOL 3.1 30.4 + - - +
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Residues in contact with ALA 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 GLU* 3.1 17.9 + - + +
9A LEU* 3.1 11.2 + - + +
11A ASP* 1.3 74.4 - - - +
13A GLN* 1.3 66.5 + - - +
14A PRO* 3.2 3.1 - - - -
15A GLN* 3.1 34.1 + - - +
16A VAL 3.7 1.9 + - - -
103B LEU* 3.8 23.8 - - + +
105B ARG* 5.6 3.4 - - - +
106B LEU* 4.0 6.7 - - + +
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Residues in contact with GLN 13 (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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9A LEU 3.0 9.8 + - - +
10A LEU* 3.5 24.2 - - - +
12A ALA* 1.3 77.7 - - - +
14A PRO* 1.3 67.4 - - + +
16A VAL* 2.9 17.2 + - + +
17A TRP* 3.1 42.1 + - + +
106B LEU* 3.7 16.7 - - + +
113B TYR 4.2 11.3 - - - +
115B ALA* 4.8 10.3 - - + +
118B LEU* 5.9 0.7 - - - +
181B GLY 5.3 0.2 - - - -
182B ASP* 2.9 37.9 + - - +
185B LEU* 4.2 16.9 - - - +
361B ARG* 4.0 0.2 - - - +
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Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.3 10.1 - - - +
11A ASP 3.3 19.5 - - - +
12A ALA 3.4 0.2 - - - -
13A GLN* 1.3 91.6 - - + +
15A GLN* 1.3 54.9 + - + +
17A TRP* 3.6 17.9 - - + +
18A HIS* 2.9 31.4 + - - +
315B SER* 6.3 0.2 - - - -
318B THR* 3.7 11.1 + - + +
359B GLY* 3.9 14.6 - - - -
360B LEU* 3.9 40.2 - - + -
403B GOL 4.5 2.5 - - - +
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Residues in contact with GLN 15 (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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11A ASP 4.4 5.4 + - - +
12A ALA* 3.1 28.3 + - - +
14A PRO* 1.3 78.3 - - + +
16A VAL* 1.3 58.1 + - - +
18A HIS* 3.4 6.6 + - - +
19A HIS* 3.1 39.4 + - + +
77B LEU 5.5 0.5 - - - +
103B LEU* 3.8 26.4 - - + +
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Residues in contact with VAL 16 (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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12A ALA 4.1 3.1 - - - +
13A GLN* 2.9 9.9 + - + +
15A GLN* 1.3 75.1 - - - +
17A TRP* 1.3 65.9 + - + +
19A HIS* 3.0 4.2 + - - +
20A PHE* 2.9 40.6 + - + -
29B LEU* 4.2 6.3 - - + -
79B TYR* 3.6 35.2 - - + +
103B LEU* 4.2 7.0 - - + -
106B LEU* 3.7 32.1 - - + -
107B LEU* 4.8 6.1 - - + -
115B ALA* 4.2 18.2 - - + -
119B THR* 4.7 1.1 - - - +
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Residues in contact with TRP 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 GLN* 3.1 49.1 + - + +
14A PRO* 3.6 23.1 - - + +
16A VAL* 1.3 76.4 - - + +
18A HIS* 1.3 54.7 + - - +
20A PHE* 3.4 32.1 - + + -
21A LEU* 2.7 50.2 + - + +
115B ALA* 5.6 2.7 - - + +
118B LEU* 3.8 15.3 - - + +
182B ASP* 3.7 7.6 - - - -
268B TRP* 3.8 22.2 - + - -
303B HIS* 4.8 0.9 - + - -
318B THR* 4.4 6.7 - - + -
322B LEU* 3.9 34.3 - - + -
359B GLY* 4.0 13.9 - - - -
360B LEU* 4.2 7.4 - - + -
361B ARG* 3.6 22.2 - - - -
401B N7I 5.2 2.0 - + - -
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Residues in contact with HIS 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 PRO 2.9 17.9 + - - +
15A GLN* 3.5 8.5 - - - +
17A TRP* 1.3 76.5 - - - +
19A HIS* 1.3 64.6 + + + +
21A LEU* 3.7 4.5 - - - -
22A GLY 3.2 9.4 + - - -
25A ASN* 4.5 3.7 + - - -
314B ASN* 5.1 2.9 - - - -
317B GLY* 4.4 5.8 - - - -
318B THR* 2.9 34.2 + - - +
321B ILE* 3.5 27.3 - - + +
402B GOL 4.3 7.4 + - - -
404B GOL 2.8 64.1 + - - -
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Residues in contact with HIS 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 GLN* 3.1 19.1 + - + +
16A VAL 3.0 7.9 + - - +
18A HIS* 1.3 81.0 - + + +
20A PHE* 1.3 63.9 + - - +
22A GLY 3.1 10.9 + - - -
25B ASN* 3.4 13.0 - - + +
26B SER 3.3 16.1 + - - -
29B LEU* 4.0 8.7 - - + -
77B LEU* 3.4 56.9 + - + +
79B TYR* 2.8 31.4 + + - +
103B LEU* 4.3 6.5 - - + -
402B GOL 4.7 13.7 + - - -
404B GOL 3.5 8.7 - - - -
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Residues in contact with PHE 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 VAL* 2.9 34.5 + - + -
17A TRP* 3.4 37.7 - + - -
19A HIS* 1.3 73.9 - - - +
21A LEU* 1.3 69.3 + - + +
22A GLY 3.2 0.7 - - - -
23A TYR* 3.5 5.9 - - - -
26B SER* 2.8 25.9 + - - +
29B LEU* 3.9 7.0 - - + -
115B ALA* 4.6 3.8 - - + -
118B LEU* 3.9 14.4 - - + -
119B THR* 3.1 47.1 - - + -
122B SER* 3.3 33.0 - - - -
123B VAL* 3.4 16.6 - - + +
401B N7I 3.3 14.8 - - - -
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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