Contacts of the strand formed by residues 61 - 67 (chain A) in PDB entry 2Z4U
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 THR 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LYS* 3.9 29.3 - - + +
54A LEU 3.1 13.5 - - - +
55A GLN* 3.9 28.0 - - + +
59A SER 4.0 4.9 - - - +
60A LYS* 1.3 80.6 - - - +
62A ILE* 1.3 64.8 + - - +
63A THR* 4.9 1.6 + - - -
78A ASP* 4.0 9.9 - - - +
79A LEU* 4.7 3.8 + - - +
148A ILE* 4.5 1.1 - - - -
152A SER* 2.8 21.9 + - - -
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Residues in contact with ILE 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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52A VAL 3.7 1.6 - - - +
53A LYS* 4.5 0.2 - - - -
54A LEU* 2.8 34.8 + - + +
61A THR* 1.3 79.7 - - - +
63A THR* 1.3 66.8 + - - +
64A LEU* 4.0 3.0 + - + -
76A TYR* 3.6 25.6 - - + -
77A SER 3.4 13.5 - - - +
78A ASP* 4.5 4.7 - - + -
148A ILE* 3.9 29.8 - - + +
151A ILE* 3.8 27.4 - - + -
152A SER* 3.9 9.9 - - - +
165A PHE* 3.8 35.4 - - + -
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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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3A THR* 5.1 2.5 - - + -
51A LEU* 3.8 31.4 - - + -
52A VAL 3.3 10.3 - - - +
53A LYS* 3.6 26.8 - - + +
61A THR* 4.9 2.4 + - - -
62A ILE* 1.3 73.6 - - - +
64A LEU* 1.4 71.5 + - - +
76A TYR* 3.0 6.7 - - - -
77A SER* 2.8 49.3 + - - -
104A LEU* 3.7 6.4 - - + +
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Residues in contact with LEU 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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50A VAL 3.9 0.2 - - - +
51A LEU* 3.3 5.4 - - - -
52A VAL* 2.8 41.4 + - + +
54A LEU* 4.1 13.9 - - + -
62A ILE* 4.4 1.6 - - + -
63A THR* 1.4 76.2 - - - +
65A MET* 1.3 59.0 + - - +
66A LEU* 3.7 16.3 + - + +
73A VAL* 4.5 21.1 - - + -
75A GLY 3.7 4.0 - - - +
76A TYR* 4.0 17.9 - - + -
165A PHE* 4.1 25.1 - - + -
166A LEU* 5.3 2.9 - - + -
169A ALA* 4.2 11.9 - - + +
170A ILE* 6.4 0.7 - - + -
173A VAL* 4.1 35.7 - - + -
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Residues in contact with MET 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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49A TYR* 3.3 44.4 - - + -
50A VAL 3.7 3.6 - - - +
51A LEU* 3.7 12.6 - - + -
63A THR 4.0 0.4 + - - -
64A LEU* 1.3 72.1 - - - +
66A LEU* 1.3 67.6 + - - +
73A VAL* 3.5 3.5 - - - -
74A MET* 2.9 34.6 + - + +
75A GLY 3.0 16.1 + - - +
99A ASP 3.8 1.3 - - - +
100A VAL* 3.6 44.9 - - + +
103A THR* 3.6 28.5 - - - +
104A LEU* 3.9 14.1 - - + -
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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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23A LEU* 4.3 10.3 - - + -
49A TYR* 3.2 7.4 - - - +
50A VAL* 2.9 40.6 + - + +
52A VAL* 4.2 22.7 - - + -
64A LEU* 3.7 30.3 - - + +
65A MET* 1.3 80.6 - - - +
67A ARG* 1.3 64.2 + - - +
71A LEU* 3.9 32.1 - - + +
72A TYR 3.4 4.7 - - - +
73A VAL* 4.0 10.8 - - + -
74A MET* 4.3 3.6 - - - -
173A VAL* 4.3 8.1 - - + -
174A SER* 3.5 19.1 - - - +
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Residues in contact with ARG 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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43A SER* 6.3 0.9 - - - -
48A LYS* 3.9 9.2 - - + +
49A TYR* 4.2 3.1 - - + -
66A LEU* 1.3 70.7 - - - +
68A ARG* 1.3 60.8 + - - +
69A ASN* 2.8 32.1 - - - +
70A ASN* 3.1 32.7 + - - +
71A LEU* 2.7 32.2 + - - +
72A TYR* 2.9 30.1 + - - +
74A MET* 3.9 21.4 - - - +
92A ILE* 3.7 19.4 - - - +
96A GLU* 2.8 42.0 + - - +
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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