Contacts of the helix formed by residues 57 - 65 (chain A) in PDB entry 4ZIN
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 ALA 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PHE* 1.3 84.9 - - - +
58A TRP* 1.3 65.5 + - - +
59A ASP* 3.2 4.1 + - + +
60A ILE* 3.4 13.9 + - + +
134A PRO 4.4 4.3 - - - +
135A VAL* 2.9 31.0 + - + +
138A LYS* 3.9 13.8 - - + +
140A THR* 3.4 27.1 - - + +
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Residues in contact with TRP 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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29A ILE* 3.6 33.0 - - + -
46A LEU* 4.0 22.9 - - + -
48A VAL* 4.2 4.9 - - + -
54A LEU* 4.0 16.4 - - + -
56A PHE* 3.3 7.3 + - - -
57A ALA* 1.3 71.9 - - - +
59A ASP* 1.3 64.9 + - - +
61A LEU* 2.9 24.1 + - + +
62A SER* 3.3 7.6 + - - -
65A PHE* 3.7 21.5 - + - -
138A LYS* 5.9 0.2 - - - +
201A ILE* 3.9 21.1 - - + -
208A TYR* 3.8 52.6 - + + -
209A THR 5.9 0.4 - - - -
211A VAL* 3.7 28.2 - - + +
213A GLN* 3.0 22.0 + - - -
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Residues in contact with ASP 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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57A ALA* 3.2 1.7 + - + -
58A TRP* 1.3 76.9 - - - +
60A ILE* 1.3 61.4 + - - +
62A SER* 3.0 21.3 + - - -
63A PRO* 3.3 0.3 - - - +
140A THR* 2.5 34.2 + - - +
141A MET 4.0 0.2 - - - -
142A GLY* 3.0 37.9 + - - -
143A 4OO 2.9 22.3 + - + -
165A LEU* 3.7 18.4 - - + -
201A ILE* 4.2 17.8 - - - +
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Residues in contact with ILE 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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22A VAL* 3.8 32.8 - - + -
56A PHE* 3.9 12.8 - - + -
57A ALA* 3.4 15.8 + - + +
58A TRP 3.0 2.0 + - - -
59A ASP* 1.3 77.6 - - - +
61A LEU* 1.3 65.4 + - + +
63A PRO* 3.8 2.1 - - - +
64A GLN* 3.0 24.3 + - - +
97A MET* 4.6 4.2 - - - +
99A PHE* 3.9 26.0 - - + -
105A VAL* 4.5 9.4 - - + +
124A LEU* 4.5 3.4 - - + +
129A PHE* 4.3 10.3 - - + -
135A VAL* 3.9 38.1 - - + -
143A 4OO 4.1 6.1 - - - -
165A LEU* 4.7 7.0 - - + -
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Residues in contact with LEU 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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18A MET* 4.1 4.0 - - + -
27A PHE* 3.7 26.2 - - + -
29A ILE* 3.5 31.2 - - + -
54A LEU* 3.7 22.0 - - + -
56A PHE* 4.0 16.4 - - + -
58A TRP* 2.9 18.4 + - + +
60A ILE* 1.3 81.7 - - + +
62A SER* 1.3 64.9 + - - +
63A PRO* 3.3 4.3 - - - -
64A GLN* 2.9 22.0 + - - +
65A PHE* 3.4 22.3 - - + -
124A LEU* 3.9 23.6 - - + -
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Residues in contact with SER 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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58A TRP* 3.3 14.5 + - - +
59A ASP* 3.0 21.5 + - - -
61A LEU* 1.3 76.6 - - - +
63A PRO* 1.4 63.3 - - - +
64A GLN 3.2 4.5 + - - -
65A PHE* 3.4 9.7 + - - -
66A CH6 3.4 4.3 - - - +
143A 4OO 3.3 14.2 - - - -
199A LEU* 3.5 11.7 - - - +
201A ILE* 4.0 10.0 - - - +
213A GLN* 3.1 44.7 + - - -
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Residues in contact with PRO 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 ASP 3.3 7.4 - - - +
60A ILE 3.8 6.3 - - - +
61A LEU 3.3 5.4 - - - -
62A SER* 1.4 95.7 - - - +
64A GLN* 1.3 63.0 + - - +
65A PHE 3.3 1.3 - - - -
66A CH6 2.9 63.5 - - + +
95A ARG* 2.9 15.4 + - - +
97A MET* 5.0 4.0 - - + -
143A 4OO 3.3 30.3 - - + +
163A GLN* 4.7 5.4 - - - +
199A LEU* 3.9 3.8 - - + -
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Residues in contact with GLN 64 (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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18A MET* 3.6 15.5 - - + -
60A ILE 3.0 20.6 + - - -
61A LEU 2.9 15.3 + - - +
63A PRO* 1.3 87.1 - - - +
65A PHE* 1.3 63.0 + - - +
66A CH6 3.5 4.0 + - - +
93A TRP* 3.6 24.5 - - + -
95A ARG* 2.9 29.8 + - - +
97A MET* 3.5 24.0 - - - -
107A VAL* 3.7 12.9 - - + +
109A GLN* 5.3 0.2 + - - -
122A VAL* 3.9 22.9 - - + +
124A LEU* 3.7 21.6 - - + +
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Residues in contact with PHE 65 (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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14A PHE* 4.1 6.8 - - - -
16A VAL* 4.0 22.7 - - + +
18A MET* 3.6 35.9 - - + -
29A ILE* 3.8 37.0 - - + -
44A ALA* 5.3 1.1 - - + -
46A LEU* 3.8 22.9 - - + -
58A TRP* 3.7 22.0 - + - -
61A LEU* 3.4 28.5 - - + -
62A SER 3.4 10.2 + - - +
63A PRO 3.3 0.8 - - - -
64A GLN* 1.3 81.6 - - - +
66A CH6 1.3 65.6 + - + +
69A SER* 3.5 15.1 - - - -
120A TYR* 3.7 18.9 - - - -
122A VAL* 5.3 0.2 - - + -
213A GLN* 4.0 11.2 - - - +
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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