Contacts of the helix formed by residues 13 - 23 (chain W) in PDB entry 2ZJR
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 PRO 13 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11W GLY 4.6 0.7 - - - +
12W ARG* 1.3 101.5 - - + +
14W GLY* 1.3 67.4 + - - +
15W ASN* 3.4 14.1 - - - +
16W GLN* 3.3 26.3 + - + +
17W VAL* 3.2 14.9 + - - +
979X A 3.9 22.9 - - - +
980X G 3.5 12.1 - - - +
85Y G 4.6 6.1 - - - +
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Residues in contact with GLY 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W PRO* 1.3 71.5 - - - +
15W ASN* 1.3 53.6 + - - +
17W VAL* 2.8 16.6 + - - +
18W LYS* 2.7 44.8 + - - +
979X A 4.2 1.0 + - - -
980X G 3.0 16.3 + - - -
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Residues in contact with ASN 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W PRO* 3.4 12.1 - - - +
14W GLY* 1.3 70.0 - - - +
16W GLN* 1.3 70.9 + - + +
18W LYS* 3.0 13.5 + - - +
19W THR* 2.9 27.7 + - - -
46W THR* 5.5 0.9 - - + -
863X C 4.1 12.7 + - - +
864X C 4.0 20.4 - - - +
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Residues in contact with GLN 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W VAL* 5.2 0.2 - - - -
12W ARG* 4.0 9.9 - - + -
13W PRO* 3.3 27.3 + - + +
15W ASN* 1.3 81.9 - - + +
17W VAL* 1.3 65.0 + - - +
19W THR* 3.3 1.2 + - - -
20W VAL* 2.8 29.4 + - - +
46W THR* 4.6 7.9 + - + +
47W VAL* 3.4 22.4 - - + -
49W HIS* 2.6 37.2 + - - -
50W LEU* 3.4 13.4 - - + +
84Y G 3.7 6.3 + - - -
85Y G 2.7 29.3 + - - -
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Residues in contact with VAL 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W VAL* 3.3 35.7 - - + +
12W ARG 3.6 13.0 - - - +
13W PRO 3.2 15.2 + - - +
14W GLY* 2.8 17.2 + - - +
16W GLN* 1.3 78.1 - - - +
18W LYS* 1.3 63.9 + - + +
20W VAL* 3.2 4.9 - - - +
21W GLN* 3.0 26.9 + - + +
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Residues in contact with LYS 18 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14W GLY* 2.7 31.7 + - - +
15W ASN* 3.2 3.7 + - - +
17W VAL* 1.3 77.3 - - + +
19W THR* 1.3 55.3 + - - +
20W VAL 3.0 1.6 - - - -
21W GLN* 2.7 36.4 + - - +
22W ALA* 2.7 20.5 + - - +
862X A 3.3 35.7 + - - +
863X C 3.2 37.1 + - - -
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Residues in contact with THR 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15W ASN 2.9 18.2 + - - -
18W LYS* 1.3 72.1 - - - +
20W VAL* 1.3 57.3 + - - +
22W ALA* 4.4 3.8 - - - -
23W LEU* 2.8 44.3 + - + +
43W MET* 3.1 36.6 - - + +
46W THR* 3.3 17.6 - - + +
47W VAL* 3.4 17.9 - - + -
863X C 2.5 30.0 + - - +
864X C 3.8 0.3 - - - -
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Residues in contact with VAL 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5W LEU* 4.1 14.6 - - + -
9W VAL* 3.8 27.1 - - + -
16W GLN 2.8 24.6 + - - +
17W VAL* 3.2 10.5 - - - +
19W THR* 1.3 78.2 - - - +
21W GLN* 1.3 65.3 + - - +
23W LEU* 3.7 5.3 + - - +
24W GLY 3.5 2.3 + - - -
25W LEU* 3.0 49.8 + - + +
47W VAL* 4.5 7.6 - - + -
50W LEU* 4.1 22.0 - - + -
51W LEU* 6.0 1.8 - - + -
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Residues in contact with GLN 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17W VAL* 3.0 14.8 + - + +
18W LYS* 2.7 27.8 + - - +
20W VAL* 1.3 68.4 - - - +
22W ALA* 1.3 57.1 + - - +
24W GLY* 2.6 31.5 + - - -
25W LEU 3.7 8.2 + - - +
861X G 5.0 7.8 + - - -
862X A 4.9 6.4 + - - +
942X U 3.6 14.7 + - - +
943X U 4.3 32.6 + - - -
944X A 5.6 0.6 + - - -
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Residues in contact with ALA 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W LYS 2.7 17.3 + - - +
19W THR* 4.0 4.7 - - - +
21W GLN* 1.3 67.0 - - - +
23W LEU* 1.3 54.4 + - - +
24W GLY 2.4 17.7 + - - -
43W MET* 3.6 20.0 - - + -
862X A 3.8 24.0 - - + +
863X C 4.4 4.9 - - - -
941X U 2.9 17.2 + - - +
942X U 2.9 30.1 + - - +
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Residues in contact with LEU 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W ILE* 5.7 4.3 - - + -
19W THR* 2.8 45.3 + - + +
20W VAL* 4.0 5.2 - - - +
22W ALA* 1.3 72.7 - - - +
24W GLY* 1.3 59.0 + - - +
25W LEU* 3.6 10.4 - - + +
32W ARG* 3.0 33.9 + - - +
34W VAL* 4.6 10.3 - - + -
40W VAL* 4.5 13.2 - - + -
43W MET* 3.1 46.0 - - + +
44W VAL* 3.9 8.7 - - + +
47W VAL* 4.1 1.3 - - + -
51W LEU* 4.0 23.3 - - + -
941X U 3.8 6.5 - - - +
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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