Contacts of the helix formed by residues 37 - 47 (chain W) in PDB entry 2ZJQ
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 37 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W SER* 2.6 30.1 + - - +
36W ASP* 1.3 77.6 - - - +
38W PRO* 1.3 66.8 - - + -
39W ALA* 3.1 2.7 - - - -
40W VAL* 2.5 33.1 + - - +
41W ARG* 2.8 14.5 + - - +
939X C 3.7 9.9 - - - +
940X G 2.6 47.0 + - - +
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Residues in contact with PRO 38 (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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37W THR* 1.3 82.7 - - + -
39W ALA* 1.3 64.6 + - + +
41W ARG* 2.4 41.3 - - - +
42W GLY* 2.9 21.7 + - - -
865X A 3.7 29.5 - - - +
866X U 5.8 0.9 - - - -
939X C 5.2 10.8 - - + +
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Residues in contact with ALA 39 (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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37W THR* 2.7 5.0 + - - -
38W PRO* 1.3 78.1 - - - +
40W VAL* 1.3 57.9 + - - +
43W MET* 3.0 14.0 + - - +
864X C 2.5 27.9 + - - +
865X A 3.5 14.8 + - - +
938X G 3.3 28.0 - - - +
939X C 6.5 0.4 - - - -
940X G 3.7 27.6 - - - +
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Residues in contact with VAL 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W LEU* 5.1 1.3 - - + -
34W VAL* 3.2 29.8 - - + -
35W SER* 2.8 29.8 - - - +
37W THR* 2.5 16.0 + - - +
39W ALA* 1.3 72.9 - - - +
41W ARG* 1.3 64.8 + - - +
42W GLY 3.0 1.1 - - - -
43W MET* 3.1 25.3 + - + +
44W VAL* 3.1 13.4 + - + +
940X G 3.0 26.2 - - + +
941X U 3.8 27.6 - - - +
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Residues in contact with ARG 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 6.4 2.0 - - - -
35W SER 5.2 0.4 - - - +
36W ASP* 2.6 66.5 + - - +
37W THR* 2.8 20.3 + - - +
38W PRO* 2.4 48.9 - - - +
40W VAL* 1.3 74.1 - - - +
42W GLY* 1.3 62.5 + - - +
44W VAL* 3.3 8.4 + - - +
45W LYS* 3.0 31.6 + - + +
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Residues in contact with GLY 42 (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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38W PRO 2.9 11.7 + - - -
41W ARG* 1.3 75.0 - - - +
43W MET* 1.3 69.6 + - - +
44W VAL 3.1 0.2 + - - -
45W LYS* 3.2 5.7 + - - -
46W THR* 2.9 24.6 + - - -
864X C 2.8 27.4 - - - -
865X A 4.0 8.3 - - - -
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Residues in contact with MET 43 (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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19W THR* 3.1 24.8 - - + +
22W ALA* 3.5 19.1 - - + -
23W LEU* 3.2 48.5 - - + +
39W ALA 3.0 12.6 - - - +
40W VAL* 3.1 19.1 - - + +
42W GLY* 1.3 76.4 - - - +
44W VAL* 1.3 64.0 + - - +
46W THR* 3.3 5.5 - - - -
47W VAL* 3.6 1.2 + - - +
863X C 3.6 9.9 - - - +
864X C 3.0 21.9 + - - +
940X G 2.9 26.5 - - - +
941X U 3.2 31.2 - - - +
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Residues in contact with VAL 44 (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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1W MET* 5.1 7.6 - - + -
3W ILE* 3.6 37.0 - - + -
23W LEU* 4.5 3.6 - - + +
34W VAL* 4.5 17.7 - - + -
40W VAL* 3.1 15.6 + - + +
41W ARG* 3.6 6.3 - - - +
43W MET* 1.3 73.3 - - + +
45W LYS* 1.3 94.8 + - - +
46W THR 3.1 0.7 + - - -
47W VAL* 3.1 6.8 + - - +
48W LYS* 2.9 20.9 + - - -
51W LEU* 4.3 11.7 - - + -
53W VAL* 3.7 15.5 - - + -
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Residues in contact with LYS 45 (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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1W MET* 5.5 7.7 - - + +
41W ARG* 3.0 21.7 + - + +
42W GLY* 3.8 6.5 - - - +
44W VAL* 1.3 114.9 - - - +
46W THR* 1.3 64.1 - - - +
48W LYS* 3.0 45.0 + - + +
53W VAL* 4.2 11.2 - - - +
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Residues in contact with THR 46 (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* 5.4 0.4 - - + -
16W GLN* 4.8 9.2 - - + +
19W THR* 3.5 17.3 - - + +
42W GLY 2.9 9.4 + - - -
43W MET 3.3 9.9 - - - -
44W VAL 3.1 0.2 + - - -
45W LYS* 1.3 80.2 - - - +
47W VAL* 1.3 76.6 + - + +
48W LYS 3.4 1.6 + - - -
49W HIS* 4.4 9.7 + - - -
864X C 2.8 38.9 + - - +
865X A 4.9 1.7 + - - -
84Y G 4.7 7.6 + - - +
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Residues in contact with VAL 47 (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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16W GLN* 3.4 46.2 - - + +
19W THR* 3.5 22.7 - - + -
20W VAL* 4.3 7.6 - - + -
23W LEU* 4.4 2.7 - - + -
43W MET 3.7 5.4 - - - +
44W VAL 3.1 1.5 + - - +
46W THR* 1.3 89.4 - - + +
48W LYS* 1.3 66.0 + - - +
49W HIS* 3.4 4.3 - - - -
50W LEU* 3.0 25.9 + - + +
51W LEU* 3.6 25.8 + - + +
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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