Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 1ZRC
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 CYS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.3 8.5 - - - +
23A TYR* 2.8 39.0 + - + +
29A LEU* 5.2 0.7 - - + -
42A ILE* 5.1 1.3 - - - -
44A LYS* 3.1 5.8 - - - +
45A GLY 3.9 2.0 - - - -
46A SER 3.4 37.9 - - - -
47A VAL* 4.0 12.8 - - + -
88A ALA* 4.0 5.6 - - - -
90A THR 3.0 21.2 + - - -
91A ALA* 1.3 73.4 - - - +
93A GLU* 1.3 60.8 - - - +
94A VAL* 3.8 18.2 - - + -
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Residues in contact with GLU 93 (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 ILE* 2.9 37.0 - - + +
21A HIS 3.6 3.4 - - - +
22A LYS* 3.9 26.1 + - + +
42A ILE 3.8 0.3 - - - -
43A VAL* 3.0 43.4 + - + +
44A LYS* 2.7 36.5 + - + +
92A CYS* 1.3 74.3 - - - +
94A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 94 (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 ILE* 4.4 3.4 - - - -
21A HIS* 2.7 41.6 + - - +
23A TYR* 3.9 22.9 - - + -
29A LEU* 3.9 11.0 - - + -
40A TYR* 3.6 32.1 - - + -
41A TYR 3.7 9.4 - - - +
42A ILE* 4.7 14.1 - - + -
47A VAL* 5.6 0.2 - - + -
70A ILE* 5.2 0.2 - - + -
92A CYS* 3.8 21.8 - - + -
93A GLU* 1.3 79.4 - - - +
95A ALA* 1.3 74.0 + - - +
96A GLU* 3.7 3.1 + - + +
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Residues in contact with ALA 95 (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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15A LEU* 3.9 28.0 - - + -
18A CYS* 4.0 15.5 - - + -
19A HIS 3.9 3.6 - - - -
20A ILE* 4.3 7.9 - - + +
39A LEU 4.6 0.2 - - - -
40A TYR* 3.4 5.7 - - - -
41A TYR* 2.9 43.3 + - + +
43A VAL* 4.0 10.7 - - + +
93A GLU 4.2 0.8 + - - -
94A VAL* 1.3 75.8 - - - +
96A GLU* 1.3 59.0 + - - +
97A ILE* 5.6 0.2 - - - -
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Residues in contact with GLU 96 (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 CYS* 3.2 4.2 - - - +
19A HIS* 2.6 48.9 + - + +
21A HIS* 3.2 35.1 + - + +
23A TYR* 2.5 35.5 + - - -
38A THR* 4.2 13.5 - - + +
39A LEU 3.5 4.5 - - - -
40A TYR* 3.4 33.9 + - + -
94A VAL 4.1 3.0 - - - +
95A ALA* 1.3 75.8 - - - +
97A ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 97 (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* 4.2 12.6 - - + -
17A HIS 3.6 14.1 - - - +
18A CYS* 3.3 23.3 - - - -
19A HIS* 5.9 0.2 - - - -
38A THR* 3.3 6.0 - - - +
39A LEU* 2.8 44.2 + - + +
95A ALA 5.6 0.2 - - - -
96A GLU* 1.3 76.7 - - - +
98A SER* 1.3 71.5 + - - +
101A LYS* 3.5 41.7 - - + +
102A PHE* 3.8 8.3 - - + +
105A LEU* 3.7 20.2 - - + -
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Residues in contact with SER 98 (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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37A GLU* 3.5 9.4 - - - -
38A THR* 4.3 3.6 - - - +
39A LEU* 5.3 0.2 - - - -
97A ILE* 1.3 81.6 - - - +
99A TYR* 1.3 66.1 + - - +
100A LYS* 3.3 8.5 + - - +
101A LYS* 2.7 29.6 + - - +
102A PHE* 2.9 19.7 + - - +
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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