Contacts of the strand formed by residues 62 - 67 (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 PHE 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.7 27.4 - - - -
48A ILE* 3.8 38.6 - - + -
49A MET* 3.8 23.1 - - + -
57A LYS 4.0 0.4 - - - +
58A GLU* 3.4 0.2 - - - -
59A ASP* 2.8 45.9 + - + +
61A ARG* 1.3 81.9 - - + +
63A THR* 1.3 60.7 + - - +
75A LEU* 4.4 10.1 - - + -
76A LEU 3.6 1.1 - - - -
77A ILE* 3.9 42.8 - - + -
78A ARG* 3.0 7.4 + - - -
84A ASP* 5.4 4.7 - - - -
88A TYR* 4.3 6.7 - + - -
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Residues in contact with THR 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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56A ASP* 3.6 36.1 - - + +
57A LYS 3.3 8.3 - - - +
58A GLU* 3.7 9.3 + - + +
62A PHE* 1.3 71.2 - - - +
64A ALA* 1.3 68.2 + - - +
65A GLN* 4.1 1.7 + - + +
74A SER 4.0 0.2 - - - +
75A LEU* 3.5 5.0 - - - -
76A LEU* 2.8 55.9 + - + +
78A ARG* 2.7 36.6 + - - -
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Residues in contact with ALA 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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36A TRP* 4.2 17.3 - - + -
49A MET* 3.7 25.2 - - + +
51A ILE* 3.7 24.5 - - + +
56A ASP* 3.4 3.3 - - - -
57A LYS 2.8 33.4 + - - +
63A THR* 1.3 76.1 - - - +
65A GLN* 1.3 59.9 + - - +
74A SER 3.2 11.0 - - - +
75A LEU* 4.4 2.0 - - + -
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Residues in contact with GLN 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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51A ILE* 4.0 2.2 - - - -
55A GLY 3.2 6.7 - - - +
56A ASP* 3.5 20.5 - - - +
63A THR* 5.1 0.7 - - + -
64A ALA* 1.3 74.5 - - - +
66A LEU* 1.3 62.1 + - - +
72A TYR* 4.2 16.5 + - + +
73A VAL* 3.2 7.0 - - - +
74A SER* 2.9 62.9 + - - +
76A LEU* 4.3 26.8 - - + +
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Residues in contact with LEU 66 (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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26A TYR* 4.1 8.5 - - - +
34A PHE* 3.7 42.6 - - + -
51A ILE* 3.7 15.9 - - + +
52A TYR* 3.7 36.1 - - - +
53A SER 3.8 9.0 - - - +
54A ASN* 3.5 5.2 - - - +
55A GLY* 3.0 29.6 + - - +
65A GLN* 1.3 74.1 - - - +
67A ASN* 1.3 62.8 + - - +
68A LYS* 3.7 17.5 - - + -
72A TYR* 3.6 15.9 - - - +
73A VAL* 3.9 13.5 - - + -
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Residues in contact with ASN 67 (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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26A TYR* 4.4 0.2 - - - -
54A ASN* 3.7 4.0 - - - +
66A LEU* 1.3 74.1 - - - +
68A LYS* 1.3 52.1 + - - +
69A ALA* 3.1 12.3 + - - +
70A SER* 2.9 32.1 + - - -
71A GLN 2.6 30.3 + - - -
72A TYR* 2.9 53.8 + - + +
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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
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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