Contacts of the helix formed by residues 3 - 20 (chain A) in PDB entry 4E70
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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2A ASP* 1.3 74.8 - - - +
4A ALA* 1.3 64.6 + - - +
6A ALA* 3.1 8.5 + - - +
7A VAL* 2.9 29.0 + - + +
1188B ARG* 4.9 4.5 - - - +
1192B SER* 3.3 35.9 - - - +
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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
----------------------------------------------------------
2A ASP* 3.3 11.0 - - - +
3A ALA* 1.3 78.3 - - - +
5A THR* 1.3 59.0 + - - +
7A VAL* 3.5 6.5 + - - +
8A GLU* 3.0 28.2 + - - +
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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
----------------------------------------------------------
1A MET* 3.6 23.3 - - + -
2A ASP* 2.6 29.8 + - - -
4A ALA* 1.3 73.3 - - - +
6A ALA* 1.3 61.0 + - - +
8A GLU* 3.3 12.5 + - - +
9A LEU* 3.0 38.7 + - + +
1105B ARG* 4.3 14.6 - - - +
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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
----------------------------------------------------------
1A MET* 3.6 19.0 - - + +
2A ASP 3.1 11.1 + - - +
3A ALA* 3.1 11.5 + - - +
5A THR* 1.3 77.9 - - - +
7A VAL* 1.3 57.0 + - - +
9A LEU* 3.4 2.1 + - - +
10A LEU* 2.9 30.2 + - - +
1185B LEU* 3.9 12.6 - - + +
1188B ARG* 3.8 30.1 - - + -
1189B ALA* 4.4 7.2 - - - +
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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
----------------------------------------------------------
3A ALA* 2.9 22.0 + - - +
4A ALA* 3.9 6.7 - - - +
6A ALA* 1.3 72.9 - - - +
8A GLU* 1.3 67.1 + - - +
10A LEU* 3.3 7.0 + - + +
11A ASP* 2.9 38.5 + - - +
1189B ALA* 3.8 25.4 - - + +
1192B SER* 5.2 3.8 - - - +
1193B LYS* 3.9 35.0 - - + +
1357B VAL 4.3 7.9 - - - +
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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 16.9 + - - +
5A THR* 3.3 13.0 + - - +
7A VAL* 1.3 77.6 - - - +
9A LEU* 1.3 62.8 + - - +
11A ASP* 3.3 7.0 + - - +
12A ALA* 3.1 22.9 + - + +
1102B PRO* 5.3 1.0 - - - +
1105B ARG* 2.7 39.1 + - - +
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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
----------------------------------------------------------
1A MET* 3.6 32.5 - - + -
5A THR* 3.0 25.4 + - + +
8A GLU* 1.3 73.8 - - - +
10A LEU* 1.3 65.8 + - - +
12A ALA* 3.1 7.0 + - + +
13A GLN* 3.0 25.6 + - - +
1102B PRO 5.1 0.9 - - - +
1105B ARG* 3.5 50.5 - - + +
1106B LEU* 4.2 14.5 - - + +
1113B TYR* 3.7 22.9 - - + +
1185B LEU* 3.9 20.6 - - + +
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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
----------------------------------------------------------
6A ALA 2.9 19.0 + - - +
7A VAL* 3.6 6.1 - - - +
9A LEU* 1.3 77.1 - - - +
11A ASP* 1.3 56.7 + - - +
13A GLN* 3.4 29.3 + - - +
14A PRO* 3.2 19.9 - - - +
1185B LEU* 4.0 9.8 - - + +
1186B PHE* 3.9 30.5 - - + +
1189B ALA* 3.5 27.1 - - + -
1357B VAL* 4.1 2.0 - - + +
1358B GLY* 3.5 29.8 - - - +
1359B GLY* 3.5 11.3 - - - +
1361B ARG* 3.6 17.9 - - - +
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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
----------------------------------------------------------
7A VAL* 2.9 32.5 + - - +
8A GLU* 3.7 6.6 - - - +
10A LEU* 1.3 75.7 - - - +
12A ALA* 1.3 56.7 + - - +
14A PRO* 3.4 14.2 - - - +
15A GLN* 4.3 7.1 - - - +
1357B VAL 5.1 0.2 - - - +
1358B GLY* 3.2 11.1 - - - -
1359B GLY 2.9 23.4 + - - -
1401B GOL 3.0 30.9 + - - +
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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
----------------------------------------------------------
8A GLU* 3.1 14.5 + - + +
9A LEU* 3.1 14.5 + - + +
11A ASP* 1.3 76.5 - - - +
13A GLN* 1.3 66.5 + - - +
14A PRO 3.3 1.1 - - - -
15A GLN* 3.0 34.9 + - - +
16A VAL 3.7 1.7 + - - -
1103B LEU* 3.9 23.0 - - + +
1105B ARG* 5.6 4.5 - - - +
1106B LEU* 4.0 8.0 - - + +
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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 17.9 + - - +
10A LEU* 3.5 22.4 - - - +
12A ALA* 1.3 77.5 - - - +
14A PRO* 1.4 69.1 - - + +
16A VAL* 2.9 17.0 + - - +
17A TRP* 3.0 35.0 + - + +
1106B LEU* 3.8 19.0 - - + +
1113B TYR 4.2 9.5 - - - +
1115B ALA* 5.3 8.0 - - + +
1181B GLY 4.6 0.3 - - - +
1182B ASP* 2.9 40.4 + - - +
1185B LEU* 3.7 23.1 - - + +
1361B 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
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10A LEU 3.2 14.1 - - - +
11A ASP 3.4 14.8 - - - +
12A ALA 3.4 0.4 - - - -
13A GLN* 1.4 89.6 - - + +
15A GLN* 1.3 55.3 + - - +
16A VAL 3.2 0.2 - - - -
17A TRP* 3.5 19.9 - - + +
18A HIS* 2.8 30.3 + - - +
1315B SER* 6.3 0.2 - - - -
1318B THR* 3.7 10.2 + - + +
1359B GLY* 4.0 13.0 - - - -
1360B LEU* 3.8 41.1 - - + -
1401B GOL 4.6 1.6 - - - +
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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 4.3 4.9 - - - +
12A ALA* 3.0 31.1 + - - +
14A PRO* 1.3 77.5 - - + +
16A VAL* 1.3 62.5 + - - +
18A HIS* 3.4 6.6 + - - +
19A HIS* 3.2 34.1 + - + +
1077B LEU 5.5 1.6 + - - -
1103B LEU* 4.2 25.7 - - + +
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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 4.2 0.2 - - - +
13A GLN* 2.9 7.3 + - - +
15A GLN* 1.3 75.0 - - - +
17A TRP* 1.3 67.5 + - + +
19A HIS* 3.0 3.8 + - - +
20A PHE* 2.9 39.1 + - + -
1029B LEU* 4.0 7.6 - - + -
1079B TYR* 3.5 33.2 - - + +
1103B LEU* 4.0 14.6 - - + -
1106B LEU* 3.8 32.3 - - + -
1107B LEU* 4.8 5.8 - - + -
1115B ALA* 4.3 15.7 - - + -
1119B THR* 4.6 1.6 - - - +
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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* 3.0 36.6 + - + +
14A PRO* 3.5 25.6 - - + +
16A VAL* 1.3 77.3 - - + +
18A HIS* 1.3 58.1 + - - +
20A PHE* 3.4 31.1 - + + -
21A LEU* 2.9 43.1 + - + +
1115B ALA* 5.6 4.6 - - + +
1118B LEU* 3.8 15.3 - - + +
1182B ASP* 3.7 19.5 - - + +
1268B TRP* 3.7 22.7 - + - -
1303B HIS* 4.8 0.9 - + - -
1318B THR* 4.3 6.1 - - + -
1322B LEU* 4.0 31.9 - - + -
1359B GLY* 4.0 15.0 - - - -
1360B LEU* 4.0 8.3 - - + -
1361B ARG* 3.5 20.4 - - - -
1402B N7I 5.2 3.1 - + - -
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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 2.8 18.3 + - - +
15A GLN* 3.6 8.3 - - - +
16A VAL 3.1 0.2 - - - -
17A TRP* 1.3 75.6 - - - +
19A HIS* 1.3 66.0 + - - +
21A LEU* 3.6 4.3 + - - -
22A GLY* 3.3 17.2 + - - -
25A ASN* 4.3 1.1 + - - -
401A GOL 3.1 28.0 - - - +
402A GOL 2.8 41.8 + - - -
1025B ASN* 5.4 1.3 + - - -
1314B ASN* 4.7 2.9 + - - -
1317B GLY* 4.3 13.0 - - - -
1318B THR* 2.9 28.7 + - - +
1321B ILE* 3.6 24.9 - - + +
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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* 3.2 18.4 + - + +
16A VAL 3.0 7.5 + - - +
18A HIS* 1.3 77.4 - - + +
20A PHE* 1.3 62.8 + - - +
22A GLY 3.0 10.9 + - - -
401A GOL 3.4 27.9 + - - -
1025B ASN* 3.5 16.1 - - + +
1026B SER* 3.4 17.8 + - - -
1029B LEU* 4.0 11.7 - - + -
1077B LEU* 3.2 56.7 + - + +
1079B TYR* 2.8 27.8 + + - -
1103B LEU* 4.3 6.3 - - + -
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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 29.5 + - + -
17A TRP* 3.4 38.8 - + - -
19A HIS* 1.3 77.4 - - - +
21A LEU* 1.3 69.6 + - + +
22A GLY 3.2 0.4 - - - -
23A TYR* 3.5 6.2 - - - -
1026B SER* 2.8 26.5 + - - +
1029B LEU* 4.0 6.1 - - + -
1115B ALA* 4.7 4.3 - - + -
1118B LEU* 3.9 14.4 - - + -
1119B THR* 3.1 47.3 - - + -
1122B SER* 3.2 32.1 - - - -
1123B VAL* 3.4 15.9 - - + +
1402B N7I 3.3 15.5 - - - -
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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