Contacts of the helix formed by residues 29 - 46 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASN* 3.6 7.5 + - - +
21A ARG* 3.1 30.1 - - - +
28A LEU* 1.3 75.0 - - - +
30A SER* 1.3 65.7 + - - +
31A ASP* 3.4 9.7 + - - +
32A THR* 2.4 36.1 + - - -
33A LEU* 2.9 27.0 + - - +
67A ASP* 3.9 13.3 + - + +
70A GLU* 3.4 24.9 + - - +
82A PHE* 5.7 2.9 - - - -
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 1.3 75.1 - - - +
31A ASP* 1.3 60.9 + - - +
33A LEU* 3.3 13.5 + - - +
34A LYS* 2.8 39.5 + - - +
70A GLU* 2.8 24.8 + - - +
82A PHE* 4.2 12.7 - - - -
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.1 1.5 - - + +
4A ASN* 6.3 0.2 - - - +
5A ASN* 4.0 10.7 + - - +
29A ASN* 3.3 12.5 + - - +
30A SER* 1.3 79.2 - - - +
32A THR* 1.3 58.8 + - - +
34A LYS* 3.4 13.5 + - - +
35A GLU* 2.9 43.4 + - - +
70A GLU* 4.9 2.8 + - - -
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Residues in contact with THR 32 (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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5A ASN* 2.9 31.3 + - + +
6A VAL* 4.3 11.0 - - + +
19A ILE* 4.4 16.2 - - + -
21A ARG* 3.8 6.0 - - - -
27A ALA 3.9 2.8 + - - +
28A LEU* 3.9 22.0 - - + -
29A ASN* 2.4 38.7 + - - -
31A ASP* 1.3 74.0 - - - +
33A LEU* 1.3 59.3 + - - +
35A GLU* 3.2 4.1 + - - +
36A MET* 2.8 32.7 + - + +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.5 19.1 - - + -
29A ASN* 2.9 19.2 + - - +
30A SER* 3.7 13.7 - - - +
32A THR* 1.3 74.7 - - - +
34A LYS* 1.3 64.0 + - + +
36A MET* 3.1 8.3 + - + +
37A ASP* 3.0 24.4 + - - +
82A PHE* 4.6 11.0 - - + -
85A LEU* 5.4 2.2 - - + -
86A GLY* 4.2 17.9 - - - +
89A VAL* 3.8 16.3 - - + +
90A PHE* 3.8 33.4 - - + -
115A ILE* 5.9 0.2 - - + -
143A PHE* 4.1 25.6 - - + -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.7 19.8 - - + +
30A SER* 2.8 30.2 + - - +
31A ASP* 3.5 13.9 - - - +
33A LEU* 1.3 77.3 - - + +
35A GLU* 1.3 63.2 + - - +
37A ASP* 3.3 9.4 + - - +
38A TYR* 3.1 20.7 + - - +
89A VAL* 5.6 0.2 - - - -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.9 21.2 - - + +
2A GLU 4.9 1.8 - - - -
3A LEU* 3.3 22.4 - - + +
4A ASN* 2.9 32.8 + - - +
5A ASN* 3.0 32.4 + - - +
6A VAL* 3.6 11.7 + - + -
31A ASP* 2.9 28.2 + - - +
32A THR 3.7 4.0 - - - +
34A LYS* 1.3 75.1 - - - +
36A MET* 1.3 52.1 + - - +
38A TYR* 3.2 9.1 + - - +
39A VAL* 2.8 40.6 + - - +
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Residues in contact with MET 36 (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 VAL* 3.8 20.6 - - + -
17A VAL* 4.2 19.1 - - + -
19A ILE* 3.5 38.4 - - + -
28A LEU* 5.7 0.9 - - + -
32A THR* 2.8 15.0 + - + +
33A LEU* 3.3 12.8 - - + +
35A GLU* 1.3 75.9 - - - +
37A ASP* 1.3 54.8 + - - +
39A VAL* 3.0 7.2 + - - +
40A ILE* 2.7 57.7 + - + +
54A LEU* 4.7 6.5 - - - -
89A VAL* 4.1 10.1 - - + -
90A PHE* 5.6 0.7 - - + -
93A LEU* 5.7 5.2 - - + -
115A ILE* 4.5 18.6 - - + -
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.0 13.0 + - - +
34A LYS* 3.3 11.0 + - - +
36A MET* 1.3 77.0 - - - +
38A TYR* 1.3 56.1 + - - +
40A ILE* 3.4 7.8 + - - +
41A GLY* 2.8 25.6 + - - -
88A LYS* 5.2 9.5 + - - +
89A VAL* 4.1 20.4 - - + +
92A ARG* 2.4 53.4 + - - +
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Residues in contact with TYR 38 (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* 3.6 61.2 + - + -
3A LEU* 3.8 28.0 - - + -
8A LEU* 6.4 0.9 - - + -
34A LYS 3.1 13.4 + - - +
35A GLU 3.2 5.8 + - - +
37A ASP* 1.3 77.4 - - - +
39A VAL* 1.3 61.6 + - + +
41A GLY* 3.2 2.3 + - - -
42A GLU* 2.7 63.5 + - + +
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Residues in contact with VAL 39 (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 LEU* 4.1 18.8 - - + -
6A VAL* 3.7 24.2 - - + -
8A LEU* 4.4 15.7 - - + -
17A VAL* 3.9 24.5 - - + -
35A GLU 2.8 37.0 + - - +
36A MET* 4.1 8.1 - - - +
38A TYR* 1.3 71.3 - - + +
40A ILE* 1.3 59.4 + - + +
42A GLU* 3.0 9.2 + - - +
43A ILE* 2.7 53.4 + - + +
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Residues in contact with ILE 40 (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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36A MET* 2.7 48.2 + - + +
37A ASP* 3.7 9.4 - - - +
39A VAL* 1.3 74.3 - - + +
41A GLY* 1.3 52.4 + - - +
43A ILE* 2.9 10.8 + - + +
44A GLU* 2.7 40.6 + - + +
89A VAL* 4.0 22.7 - - + +
92A ARG* 3.9 35.9 - - + +
93A LEU* 4.0 27.6 - - + +
96A LEU* 4.5 13.6 - - + +
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Residues in contact with GLY 41 (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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37A ASP 2.8 12.4 + - - -
38A TYR* 3.6 3.4 - - - -
40A ILE* 1.3 75.9 - - - +
42A GLU* 1.3 61.5 + - - +
44A GLU* 3.3 8.6 + - - +
45A ASN* 3.2 31.9 + - - +
92A ARG* 3.3 25.5 - - - +
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.3 19.1 - - + -
10A LYS* 5.0 7.7 + - - +
38A TYR* 2.7 54.7 + - + +
39A VAL* 3.2 13.7 - - - +
41A GLY* 1.3 72.9 - - - +
43A ILE* 1.3 61.8 + - - +
45A ASN* 3.3 17.2 + - - +
46A ASP* 3.4 13.9 + - - +
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Residues in contact with ILE 43 (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 LEU* 3.9 16.8 - - + -
15A ALA* 4.4 7.9 - - + -
17A VAL* 3.7 29.6 - - + -
39A VAL* 2.7 31.0 + - + +
40A ILE* 2.9 9.8 + - + +
42A GLU* 1.3 70.3 - - - +
44A GLU* 1.3 68.8 + - - +
46A ASP* 3.1 17.6 + - - +
49A VAL* 3.6 26.0 - - + -
52A VAL* 3.8 23.3 - - + -
96A LEU* 4.3 9.0 - - + -
98A LYS* 3.4 21.0 - - + -
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Residues in contact with GLU 44 (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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40A ILE* 2.7 15.5 + - + +
41A GLY* 3.3 10.5 - - - +
42A GLU 3.2 0.2 - - - -
43A ILE* 1.3 79.3 - - - +
45A ASN* 1.3 65.2 + - - +
46A ASP 3.5 0.2 + - - -
47A SER 5.2 0.2 + - - -
92A ARG* 3.2 53.0 + - - +
96A LEU* 3.6 26.6 - - + +
98A LYS* 3.8 12.8 + - - +
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Residues in contact with ASN 45 (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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41A GLY 3.2 19.9 + - - +
42A GLU* 3.3 9.1 + - - +
43A ILE 3.2 0.4 - - - -
44A GLU* 1.3 83.2 - - - +
46A ASP* 1.3 58.1 + - - +
47A SER* 3.4 9.3 + - - -
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Residues in contact with ASP 46 (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 LYS* 4.3 22.0 + - - +
42A GLU 3.4 14.3 + - - +
43A ILE* 3.1 6.9 + - - +
45A ASN* 1.3 74.7 - - - +
47A SER* 1.3 58.2 + - - +
48A GLU* 2.9 31.0 + - - +
49A VAL* 3.0 41.0 + - + +
98A LYS* 3.3 13.9 + - - -
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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
------------------------------------------------------------
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