Contacts of the helix formed by residues 29 - 45 (chain B) in PDB entry 5Z7R
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 ASN 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN* 4.8 3.8 - - - +
21B ARG* 3.0 33.8 - - - +
28B LEU* 1.3 76.3 - - - +
30B SER* 1.3 69.3 + - - +
31B ASP* 3.4 9.1 + - - +
32B THR* 2.7 44.5 + - - -
33B LEU* 2.8 27.8 + - - +
66B ALA* 5.6 0.4 - - - -
67B ASP* 4.1 9.8 - - + +
70B GLU* 3.6 20.3 + - - +
82B PHE* 5.2 5.8 - - - -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 1.3 75.3 - - - +
31B ASP* 1.3 65.2 + - - +
33B LEU* 3.2 6.8 + - - +
34B LYS* 3.0 41.4 + - - +
70B GLU* 2.5 28.5 + - - +
82B PHE* 4.4 15.4 - - - -
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASN* 5.7 4.1 + - - +
5B ASN* 4.1 14.3 + - - +
29B ASN* 3.2 10.1 + - - +
30B SER* 1.3 85.8 - - - +
32B THR* 1.3 58.1 + - - +
34B LYS* 3.3 12.6 + - - +
35B GLU* 3.0 34.8 + - - +
70B GLU* 5.3 0.2 + - - -
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN* 3.2 34.7 + - + +
6B VAL* 4.2 11.2 - - + +
19B ILE* 4.4 14.1 - - + -
21B ARG* 3.6 5.0 - - - -
27B ALA 4.4 7.0 - - - +
28B LEU* 4.3 20.9 - - + -
29B ASN* 2.7 37.3 + - - -
31B ASP* 1.3 72.7 - - - +
33B LEU* 1.3 58.7 + - - +
35B GLU* 3.4 7.0 + - - +
36B MET* 3.0 28.3 + - + +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.3 17.5 - - + -
29B ASN 2.8 21.2 + - - +
30B SER* 3.4 8.5 - - - +
32B THR* 1.3 74.8 - - - +
34B LYS* 1.3 63.7 + - - +
36B MET* 3.3 6.5 + - + +
37B ASP* 3.2 21.3 + - - +
82B PHE* 4.5 15.5 - - + -
85B LEU* 5.2 2.0 - - + -
86B GLY* 4.0 19.3 - - - +
89B VAL* 3.8 17.1 - - + +
90B PHE* 3.8 32.3 - - + -
143B PHE* 3.9 26.2 - - + -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.9 22.5 - - + +
30B SER* 3.0 35.9 + - - +
31B ASP* 3.3 12.1 + - - +
33B LEU* 1.3 75.5 - - - +
35B GLU* 1.3 61.7 + - - +
37B ASP* 3.3 9.1 + - - +
38B TYR* 3.0 22.5 + - - +
85B LEU* 4.7 17.6 - - - +
89B VAL* 5.8 0.2 - - - -
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.4 9.0 - - - -
2B GLU 3.7 8.5 - - - +
3B LEU* 3.9 19.2 - - + -
4B ASN* 2.8 36.0 + - - +
5B ASN* 2.9 30.5 + - - -
6B VAL* 3.0 27.6 + - + +
31B ASP* 3.0 21.1 + - + +
32B THR 3.7 1.6 - - - +
33B LEU 3.3 0.2 - - - -
34B LYS* 1.3 76.7 - - + +
36B MET* 1.3 58.5 + - - +
38B TYR* 3.4 7.8 + - - +
39B VAL* 3.0 35.6 + - - +
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Residues in contact with MET 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.6 24.2 - - + -
17B VAL* 3.9 17.9 - - + -
19B ILE* 3.1 36.3 - - + -
28B LEU* 6.0 2.2 - - + -
32B THR* 3.0 16.5 + - + +
33B LEU* 3.6 9.2 - - + +
34B LYS 3.2 0.2 - - - -
35B GLU* 1.3 74.2 - - - +
37B ASP* 1.3 58.5 + - - +
39B VAL* 3.2 11.5 - - - +
40B ILE* 2.9 44.1 + - + +
54B LEU* 4.6 8.3 - - - -
89B VAL* 4.0 15.9 - - + -
90B PHE* 5.5 0.9 - - + -
93B LEU* 5.9 4.0 - - + -
115B ILE* 4.5 17.7 - - + -
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 3.2 12.7 + - - +
34B LYS* 3.4 13.0 - - - +
36B MET* 1.3 76.1 - - - +
38B TYR* 1.3 62.0 + - - +
40B ILE* 3.4 5.0 + - - +
41B GLY* 3.2 11.3 + - - -
88B LYS* 3.3 24.1 + - - -
89B VAL* 3.6 22.6 - - + +
92B ARG* 3.1 49.2 + - - -
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.9 55.4 + - + -
3B LEU* 4.1 25.8 - - + -
34B LYS 3.0 13.6 + - - +
35B GLU 3.6 7.4 - - - +
36B MET 3.3 0.2 - - - -
37B ASP* 1.3 76.8 + - - +
39B VAL* 1.3 66.5 + - + +
41B GLY* 3.2 5.8 + - - -
42B GLU* 3.0 54.2 + - + +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.6 13.0 - - + -
6B VAL* 4.5 13.7 - - + -
8B LEU* 4.6 23.3 - - + +
17B VAL* 4.4 17.5 - - + -
35B GLU 3.0 17.9 + - - +
36B MET* 3.2 30.1 - - - +
38B TYR* 1.3 82.2 - - + +
40B ILE* 1.3 75.4 + - + +
42B GLU* 3.2 7.7 + - - +
43B ILE* 2.9 30.3 + - + +
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 6.4 0.4 - - + -
36B MET* 2.9 41.6 + - + +
37B ASP* 3.5 9.9 - - - +
38B TYR 3.3 0.2 - - - -
39B VAL* 1.3 84.5 - - + +
41B GLY* 1.3 56.9 + - - +
43B ILE* 3.3 8.8 + - + +
44B GLU* 2.9 29.9 + - - +
89B VAL* 4.8 9.6 - - + +
92B ARG* 4.0 34.1 - - + +
93B LEU* 3.3 35.9 - - + -
96B LEU* 3.9 23.6 - - + +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASP 3.2 9.4 + - - -
38B TYR* 3.2 5.4 + - - -
40B ILE* 1.3 75.4 - - - +
42B GLU* 1.3 65.2 + - - +
44B GLU* 3.1 5.7 + - - +
45B ASN* 2.8 34.8 + - - -
92B ARG* 3.6 20.3 - - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.1 24.7 - - + -
10B LYS* 5.2 10.1 + - - +
38B TYR* 3.0 57.1 + - + +
39B VAL* 3.2 9.8 + - - +
41B GLY* 1.3 73.7 - - - +
43B ILE* 1.3 63.7 + - - +
45B ASN* 3.2 22.9 + - - +
46B ASP* 3.3 15.8 + - - +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.6 32.5 - - + -
10B LYS* 5.8 2.2 - - + -
15B ALA* 4.3 13.2 - - + -
17B VAL* 3.8 18.6 - - + -
39B VAL* 2.9 23.7 + - + +
40B ILE* 3.5 7.4 - - + +
42B GLU* 1.3 80.1 - - - +
44B GLU* 1.3 61.5 + - - +
46B ASP* 3.1 16.8 + - - +
49B VAL* 4.4 8.8 - - + +
52B VAL* 4.0 17.5 - - + -
96B LEU* 3.8 26.0 - - + -
98B LYS* 3.0 30.4 - - + -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 2.9 16.4 + - - +
41B GLY* 3.2 15.1 - - - +
43B ILE* 1.3 76.8 - - - +
45B ASN* 1.3 64.6 + - - +
46B ASP 3.1 4.5 + - - +
47B SER* 5.0 0.7 + - - -
92B ARG* 2.6 39.3 + - - +
96B LEU* 3.6 20.1 - - + +
97B GLU 5.9 0.4 - - - +
98B LYS* 4.1 10.8 + - - +
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLY* 2.8 25.2 + - - +
42B GLU* 3.2 16.7 + - - +
44B GLU* 1.3 81.0 - - - +
46B ASP* 1.3 56.3 + - - +
47B SER 4.0 1.8 + - - -
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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
------------------------------------------------------------
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