Contacts of the helix formed by residues 51 - 63 (chain A) in PDB entry 3ZWH
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 ASP 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ARG* 3.4 6.0 + - - +
50A THR* 1.3 76.4 - - - +
52A GLU* 1.3 64.1 + - - +
53A ALA* 3.4 11.1 + - - +
54A ALA* 3.1 30.2 + - + +
55A PHE* 3.1 20.0 + - - +
1095A ACT 5.0 9.5 + - - +
1096A ACT 5.2 1.0 - - + +
1897Q GLN* 3.2 31.8 + - - +
1898Q ARG* 4.6 7.1 + - - -
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Residues in contact with GLU 52 (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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31A LYS* 4.9 8.5 - - - +
35A LYS* 3.3 27.5 + - - -
51A ASP* 1.3 73.0 + - - +
53A ALA* 1.3 57.7 + - - +
55A PHE* 3.1 19.6 + - - +
56A GLN* 2.9 33.7 + - + +
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Residues in contact with ALA 53 (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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51A ASP* 3.3 8.7 + - - +
52A GLU* 1.3 78.6 - - - +
54A ALA* 1.3 62.8 + - - +
56A GLN* 3.4 6.8 + - - +
57A LYS* 3.0 24.1 + - - +
1898Q ARG* 4.0 13.9 + - - +
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Residues in contact with ALA 54 (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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51A ASP* 3.1 36.5 + - + +
53A ALA* 1.3 77.7 - - - +
55A PHE* 1.3 62.3 + - - +
57A LYS* 3.2 4.2 + - - +
58A LEU* 3.0 21.1 + - - +
1096A ACT 4.3 12.4 - - + +
1897Q GLN* 5.0 2.0 - - - +
1898Q ARG* 3.8 36.0 - - + +
1901Q GLU* 4.7 3.1 - - - +
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Residues in contact with PHE 55 (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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31A LYS* 3.4 47.8 - - + -
34A LEU* 4.0 24.9 - - + -
35A LYS* 3.5 39.3 - - + -
38A LEU* 4.4 10.5 - - + -
51A ASP 3.1 11.7 + - - +
52A GLU* 3.1 24.6 + - - +
54A ALA* 1.3 77.0 - - - +
56A GLN* 1.3 64.6 + - - +
58A LEU* 3.1 7.8 + - + +
59A MET* 3.0 21.6 + - + +
1095A ACT 4.1 17.0 - - + +
1096A ACT 3.7 23.7 - - + +
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Residues in contact with GLN 56 (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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31A LYS* 3.0 35.9 - - - +
52A GLU* 2.9 21.7 + - + +
53A ALA* 3.7 7.9 - - - +
55A PHE* 1.3 80.1 - - - +
57A LYS* 1.3 62.4 + - - +
59A MET* 3.3 13.4 + - - +
60A SER* 3.0 29.2 + - - +
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Residues in contact with LYS 57 (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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53A ALA 3.0 14.5 + - - +
54A ALA 3.4 8.5 - - - +
56A GLN* 1.3 77.6 - - - +
58A LEU* 1.3 56.4 + - - +
60A SER* 3.2 13.2 + - - -
61A ASN* 2.9 48.8 + - - +
1898Q ARG* 3.9 9.0 - - - +
1901Q GLU* 3.2 40.7 + - + +
1905Q GLU* 3.6 14.1 + - - -
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Residues in contact with LEU 58 (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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34A LEU* 5.1 3.6 - - + -
38A LEU* 3.9 18.2 - - + -
54A ALA 3.0 12.7 + - - +
55A PHE* 3.4 14.8 - - + +
57A LYS* 1.3 74.9 - - - +
59A MET* 1.3 66.9 + - - +
61A ASN* 3.1 5.5 + - - +
62A LEU* 3.0 45.8 + - + +
78A PHE* 4.1 17.7 - - + -
1096A ACT 4.2 8.1 - - + -
1900Q LEU* 3.9 41.3 - - + +
1901Q GLU* 4.5 6.9 - - + +
1904Q THR* 3.8 20.0 - - - +
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Residues in contact with MET 59 (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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29A LEU 4.2 1.8 - - - +
31A LYS* 3.9 47.8 - - + +
34A LEU* 3.7 30.2 - - + +
55A PHE* 3.0 13.0 + - + +
56A GLN* 3.4 19.5 - - - +
58A LEU* 1.3 76.1 - - - +
60A SER* 1.3 57.6 + - - +
62A LEU* 3.3 3.8 + - - +
63A ASP* 3.0 32.3 + - + +
68A ASN* 3.6 35.0 - - - +
69A GLU* 4.0 5.4 - - - +
70A VAL* 3.9 21.8 - - + -
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Residues in contact with SER 60 (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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56A GLN* 3.0 27.8 + - - +
57A LYS* 3.5 17.4 - - - -
59A MET* 1.3 75.3 - - - +
61A ASN* 1.3 66.9 + - - +
63A ASP* 3.5 19.1 + - - +
64A SER* 5.5 0.2 - - - -
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Residues in contact with ASN 61 (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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57A LYS* 2.9 35.3 + - - +
58A LEU* 3.1 8.0 + - - +
60A SER* 1.3 77.6 - - - +
62A LEU* 1.3 61.9 + - - +
64A SER* 4.0 5.5 + - - -
1901Q GLU* 3.2 25.3 + - - +
1904Q THR* 3.1 40.2 + - - +
1905Q GLU* 3.3 17.5 + - - +
1907Q ALA* 3.4 20.5 - - - +
1908Q ASP* 4.4 4.3 - - - +
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Residues in contact with LEU 62 (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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34A LEU* 4.1 26.0 - - + -
58A LEU* 3.0 28.1 + - + +
59A MET 3.9 3.8 - - - +
61A ASN* 1.3 74.5 - - - +
63A ASP* 1.3 56.2 + - - +
64A SER* 2.8 15.8 + - - -
70A VAL* 4.3 17.7 - - + -
74A GLU* 3.4 26.7 - - - +
77A VAL* 5.7 0.4 - - + -
78A PHE* 3.6 56.8 - - + +
1904Q THR* 3.7 23.8 - - + -
1907Q ALA* 4.8 6.3 - - + -
1911Q ASN* 4.5 1.6 + - - -
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Residues in contact with ASP 63 (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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59A MET* 3.0 22.8 + - + +
60A SER* 3.5 13.7 + - - +
61A ASN 3.4 0.8 - - - -
62A LEU* 1.3 71.4 - - - +
64A SER* 1.3 61.7 + - - +
66A ARG* 3.2 14.5 + - - +
67A ASP 3.1 14.5 + - - -
68A ASN* 2.8 32.2 + - - -
69A GLU 3.6 8.5 - - - +
70A VAL* 5.0 0.6 - - + +
74A GLU* 3.9 4.3 - - - -
502A CA 2.5 28.5 - - - -
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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