Contacts of the strand formed by residues 115 - 122 (chain B) 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 PHE 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU 3.4 5.5 - - - +
20B ARG* 3.9 9.2 - - - +
21B MET 2.9 23.5 + - - +
62B ASP* 5.9 0.2 - - - -
63B LEU* 3.5 47.6 - - + +
65B TRP* 3.2 46.5 - + + +
98B ILE* 3.1 28.7 - - + -
109B ARG* 4.9 13.7 - - + -
110B ASP 4.7 1.8 - - - -
113B TRP* 4.0 19.7 - + + -
114B THR* 1.3 89.8 - - - +
116B SER* 1.3 68.4 + - - +
117B PHE* 4.3 2.3 - - - -
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE 4.0 9.3 + - - -
18B LYS* 4.4 3.1 + - - -
19B GLU 3.3 12.8 + - - -
20B ARG* 3.6 18.4 + - - +
59B LEU* 3.9 27.9 - - - +
60B LYS* 4.8 0.9 - - - +
62B ASP* 3.6 15.1 + - - -
63B LEU 3.4 13.6 + - - -
64B VAL* 4.1 1.8 - - - -
65B TRP* 3.0 23.0 + - - -
115B PHE* 1.3 80.7 - - - +
117B PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.8 1.6 - - - +
17B PHE* 3.1 58.3 + + + +
19B GLU* 3.0 43.5 - - + -
21B MET* 3.1 42.0 - - + -
26B ALA* 3.4 27.1 - - + -
29B PHE* 3.9 10.5 - + - -
30B CYS* 5.0 2.7 - - - -
39B LEU* 3.8 19.1 - - + -
64B VAL* 4.6 0.2 - - - -
65B TRP* 4.4 4.9 - - + +
115B PHE 4.3 2.9 - - - -
116B SER* 1.3 81.6 - - - +
118B VAL* 1.3 70.4 + - - +
119B CYS 4.1 0.7 - - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 4.5 12.6 - - + -
15B LYS 3.5 16.8 - - - +
16B VAL* 4.2 15.5 - - + -
30B CYS* 4.5 0.9 - - - -
39B LEU* 3.6 2.3 - - - +
40B VAL* 2.6 49.5 + - + +
51B VAL* 4.1 23.3 - - + -
55B ALA* 4.3 11.9 - - + +
59B LEU* 4.6 2.0 - - + -
64B VAL* 4.2 23.8 - - + -
65B TRP 4.8 4.0 + - - -
117B PHE* 1.3 81.0 - - - +
119B CYS* 1.3 59.8 + - - +
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Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TRP* 4.6 14.6 - - + -
13B CYS 3.9 0.2 - - - +
14B TYR* 3.6 4.5 - - - -
15B LYS 3.2 26.5 + - - +
17B PHE* 3.4 30.5 - - + -
29B PHE* 4.5 3.8 - - - -
30B CYS* 2.0 56.3 - - + +
33B GLN* 4.3 3.6 - - - -
37B GLY* 5.4 1.8 - - - -
38B HIS 3.2 8.5 - - - +
117B PHE* 4.1 1.1 - - - -
118B VAL* 1.3 77.8 - - - +
120B LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 5.2 2.4 + - - -
6B TRP* 5.1 1.1 - - - -
12B TYR* 3.9 23.3 - - + -
13B CYS 3.3 9.9 - - - +
14B TYR* 3.4 40.6 - - + -
36B ASP 3.6 2.3 - - - +
37B GLY* 3.5 1.2 - - - -
38B HIS* 2.7 33.3 + - - +
39B LEU 4.9 0.4 - - - +
40B VAL* 3.9 10.8 - - - -
41B SER* 2.8 40.1 + - - +
43B ARG* 4.4 14.5 - - - +
47B GLU* 3.1 19.4 + - - -
119B CYS* 1.3 76.3 - - - +
121B CYS* 1.3 66.2 + - - +
122B PRO* 4.5 6.1 - - + +
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Residues in contact with CYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TRP* 4.5 9.2 - - - -
12B TYR* 4.6 1.3 - - - -
13B CYS* 3.0 41.7 + - - +
34B HIS* 3.8 34.8 - - - -
35B LYS 3.5 3.6 - - - +
36B ASP* 3.3 22.9 - - + +
37B GLY* 3.5 8.5 - - - -
120B LYS* 1.3 76.7 - - - +
122B PRO* 1.3 73.4 - - + +
123B ALA* 3.4 1.1 + - - -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY 3.5 8.3 - - - +
12B TYR* 3.8 27.6 - - + -
36B ASP* 4.0 20.6 - - + +
43B ARG* 6.0 0.2 - - - +
120B LYS* 4.5 6.5 - - + +
121B CYS* 1.3 88.3 - - + +
123B ALA* 1.3 69.7 + - - +
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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