Contacts of the strand formed by residues 12 - 21 (chain A) in PDB entry 1OZ7
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A CYS* 4.2 0.4 - - - -
8A SER* 3.1 7.4 + - - -
9A ASN 2.8 37.0 + - - +
10A GLY* 3.2 19.1 - - - -
11A VAL* 1.3 76.3 - - + +
13A CYS* 1.3 64.0 + - - +
14A TYR* 3.3 19.3 - - + -
43A GLU* 5.2 7.3 + - - -
47A GLU* 6.2 0.2 - - - -
126A LYS* 3.7 33.9 - - + -
127A TYR* 3.6 19.1 - - - -
128A PRO* 3.5 33.0 - - + +
81B ASP* 5.6 1.9 + - - -
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Residues in contact with CYS 13 (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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2A CYS* 2.0 49.6 - - + -
6A TRP* 4.0 7.1 - - + -
7A SER 3.2 4.5 - - - -
12A TYR* 1.3 70.2 - - - +
14A TYR* 1.3 63.5 + - - +
126A LYS* 3.2 6.8 - - - +
127A TYR* 3.0 59.5 + - + +
129A VAL* 3.2 29.2 - - - -
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Residues in contact with TYR 14 (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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5A GLY 4.9 0.3 - - - +
6A TRP* 3.6 4.7 - - - -
7A SER* 2.7 49.1 + - - +
9A ASN* 3.5 30.9 + - + -
12A TYR* 3.3 42.9 - - + +
13A CYS* 1.3 77.6 - - - +
15A MET* 1.3 63.1 + - - +
40A LEU* 5.0 4.7 - - + -
41A SER 5.1 0.7 - - - -
47A GLU* 2.6 42.1 + - + +
50A LEU* 4.3 14.4 - - + -
51A VAL* 4.3 15.9 - - + -
54A VAL* 5.1 11.9 - - + +
124A MET* 6.2 2.5 - - + -
125A CYS 3.4 7.6 - - - +
126A LYS* 3.6 23.1 - - + -
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Residues in contact with MET 15 (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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4A PRO 4.9 0.7 - - - +
5A GLY* 3.0 33.9 - - - +
6A TRP* 3.5 36.9 - - + -
14A TYR* 1.3 78.2 - - - +
16A LEU* 1.3 70.9 + - - +
17A PHE* 3.5 38.5 - - + -
54A VAL* 5.4 3.4 - - - -
58A ASN* 6.2 1.8 - - - +
124A MET* 3.3 3.3 - - - -
125A CYS 2.7 38.2 + - - -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A MET* 1.3 86.3 - - - +
17A PHE* 1.3 61.4 + - - +
18A LYS 4.1 0.9 + - - -
54A VAL* 4.1 32.5 - - + +
55A VAL* 4.6 1.6 - - + -
58A ASN* 4.5 14.2 - - + +
59A ILE* 3.5 30.1 - - + +
123A PHE 3.3 6.3 - - - +
124A MET* 4.1 4.9 - - + +
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Residues in contact with PHE 17 (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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6A TRP* 3.9 14.1 - + - -
15A MET* 3.5 49.8 - - + -
16A LEU* 1.3 72.6 - - - +
18A LYS* 1.3 57.6 + - - +
19A GLU* 2.9 18.8 + - + -
29A PHE* 4.0 22.9 - + - -
33A GLN* 4.9 3.6 - - + -
59A ILE* 4.5 2.0 - - - -
122A PRO* 3.4 4.0 - - - +
123A PHE* 2.7 58.5 + + + -
125A CYS* 3.5 33.2 - - + -
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU 4.1 1.8 + - - -
17A PHE* 1.3 68.2 - - - +
19A GLU* 1.3 70.0 + - - +
20A PRO* 3.9 12.1 - - - +
58A ASN 4.5 13.0 + - - +
59A ILE* 3.4 20.9 - - + +
60A GLY* 2.2 39.4 + - - +
61A LYS 3.0 16.4 + - - -
62A MET* 3.6 13.7 - - - +
122A PRO* 3.9 9.9 - - + +
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Residues in contact with GLU 19 (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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17A PHE* 2.9 20.4 + - + -
18A LYS* 1.3 87.1 - - - +
20A PRO* 1.3 70.7 - - - +
21A LYS* 3.3 18.6 + - - +
29A PHE* 5.8 5.8 - - + -
122A PRO* 4.3 2.9 - - - +
123A PHE* 3.1 29.5 - - + -
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Residues in contact with PRO 20 (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 LYS* 3.9 11.4 - - + +
19A GLU* 1.3 82.8 - - - +
21A LYS* 1.3 66.7 + - - +
120A THR* 3.9 29.7 - - - +
121A PHE 3.7 10.3 - - - +
122A PRO* 4.5 14.1 - - + -
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Residues in contact with LYS 21 (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 GLU* 3.3 22.1 + - - +
20A PRO* 1.3 80.8 + - - +
22A THR* 1.3 68.7 + - - +
25A GLU* 4.0 17.7 - - + +
26A ALA* 4.0 26.2 - - + +
29A PHE* 3.7 32.3 - - - -
66A TRP* 3.0 13.8 + - - -
119A ASN 3.1 0.9 - - - +
120A THR* 3.6 10.8 - - - +
121A PHE 2.9 24.7 + - - +
123A PHE* 4.0 12.3 - - + -
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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