Contacts of the strand formed by residues 72 - 77 (chain A) in PDB entry 4ZDH
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 TYR 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.4 25.8 - - - +
24A CYS 3.3 12.1 - - - +
25A THR* 4.1 11.9 - - + -
26A TYR* 3.4 7.0 - - - -
65A GLN* 4.3 18.1 + - + -
66A LEU* 3.6 4.6 - - - +
67A ASN* 2.9 72.2 + - + +
70A SER* 3.8 20.6 - - - +
71A GLN* 1.3 74.8 - - - +
73A VAL* 1.3 61.4 + - - +
74A SER* 3.5 14.4 - - - -
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Residues in contact with VAL 73 (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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23A ASN* 3.0 2.3 - - - +
24A CYS* 2.8 58.9 + - + +
26A TYR* 5.0 2.5 - - + -
34A PHE* 4.1 21.3 - - + -
35A PHE 5.8 1.1 - - - +
36A TRP* 3.8 19.5 - - + +
51A ILE* 3.9 24.9 - - + -
65A GLN 3.2 14.1 - - - +
66A LEU* 3.9 13.9 - - + -
72A TYR* 1.3 74.5 - - - +
74A SER* 1.3 66.7 + - - +
90A CYS* 4.7 2.9 - - + -
91A ALA 5.9 0.4 - - - +
92A VAL* 5.2 2.2 - - + -
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Residues in contact with SER 74 (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 LEU 3.1 14.1 - - - -
23A ASN* 2.7 23.3 + - - -
36A TRP* 3.3 13.0 + - - -
64A ALA* 3.2 5.7 - - - -
65A GLN* 2.9 60.4 + - - +
72A TYR* 3.5 7.8 - - - -
73A VAL* 1.3 73.0 - - - +
75A LEU* 1.3 59.5 + - - +
76A LEU* 4.5 6.5 - - - -
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Residues in contact with LEU 75 (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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20A ALA 3.7 1.2 - - - +
21A SER* 3.3 3.8 - - - -
22A LEU* 2.9 56.3 + - + +
36A TRP* 3.6 32.5 - - + -
48A ILE* 3.8 12.8 - - + -
49A MET* 4.1 25.4 - - + -
62A PHE* 4.4 11.7 - - + -
63A THR 3.5 16.2 - - - +
64A ALA 4.4 0.4 - - - +
74A SER* 1.3 74.3 - - - +
76A LEU* 1.3 67.5 + - - +
77A ILE* 4.6 7.0 - - + -
88A TYR* 3.8 22.9 - - + -
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Residues in contact with LEU 76 (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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19A ILE* 4.0 22.9 - - + -
20A ALA 3.4 3.4 - - - -
21A SER* 3.7 18.8 - - - -
61A ARG 3.6 2.9 - - - +
62A PHE* 3.6 3.1 - - - -
63A THR* 2.8 55.7 + - + +
65A GLN* 4.3 33.2 - - + +
74A SER* 4.5 6.7 - - - -
75A LEU* 1.3 80.2 - - - +
77A ILE* 1.3 63.0 + - - +
78A ARG* 3.8 6.2 - - + +
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Residues in contact with ILE 77 (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 ALA 3.7 1.9 - - - +
19A ILE* 3.3 5.3 - - - +
20A ALA* 2.7 52.2 + - + +
22A LEU* 5.1 4.3 - - + -
61A ARG* 3.6 28.7 - - + +
62A PHE* 3.9 28.0 - - + -
75A LEU* 4.6 8.7 - - + +
76A LEU* 1.3 75.2 - - - +
78A ARG* 1.3 62.4 + - - +
80A ALA* 4.1 4.5 + - + +
84A ASP* 3.7 18.6 - - + +
88A TYR* 3.6 41.1 - - + +
108A VAL* 5.5 2.5 - - + -
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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