Contacts of the strand formed by residues 91 - 99 (chain B) in PDB entry 1YZZ
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 GLY 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 5.7 0.2 - - - -
39B GLN 3.3 12.6 - - - -
40B ALA* 4.4 2.0 - - - -
41B PRO* 4.7 4.3 - - - -
89B ASP 3.7 1.0 + - - -
90B THR* 1.3 80.3 - - - +
92B MET* 1.3 60.9 + - - -
93B TYR* 3.6 10.1 - - - -
113B GLN* 3.1 11.5 + - - -
114B VAL 2.8 33.2 + - - +
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Residues in contact with MET 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 3.2 3.8 - - - +
39B GLN* 2.8 42.0 + - + +
91B GLY* 1.3 72.5 - - - -
93B TYR* 1.3 61.3 + - - +
94B TYR* 3.4 35.4 - - + +
110B GLN 4.3 6.5 - - - +
111B GLY* 3.9 25.8 - - - +
112B THR 3.8 2.9 - - - +
113B GLN* 3.6 34.7 + - + +
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Residues in contact with TYR 93 (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 GLU* 3.7 2.4 - - - +
20B LEU* 3.9 27.1 - - + -
36B TRP* 4.3 7.0 - + + -
37B VAL 3.6 4.3 - - - +
38B ARG* 3.1 44.3 - - + -
48B VAL* 4.3 13.7 - - + -
67B PHE* 4.7 3.7 - + - -
80B LEU* 4.8 6.5 - - + -
82B MET* 3.8 22.4 - - - -
85B LEU* 5.5 0.2 - - - +
89B ASP* 2.5 33.7 + - - +
90B THR 4.7 0.4 - - - -
91B GLY* 3.6 14.1 - - - -
92B MET* 1.3 77.4 - - - +
94B TYR* 1.3 62.6 + - - +
111B GLY* 3.3 1.7 - - - -
112B THR* 2.9 42.1 + - + +
114B VAL* 3.7 23.1 - - + +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 3.3 15.3 + - - -
43A LYS 4.8 0.3 + - - -
44A GLY* 4.7 8.7 - - - -
45A LEU* 4.3 27.1 - - + -
6B GLU* 3.3 7.9 - - - -
36B TRP* 3.3 5.8 - - - -
37B VAL* 2.8 52.5 + - + +
39B GLN* 3.2 29.8 + - + -
45B LEU* 4.9 0.9 - - + -
92B MET* 3.4 35.4 - - + +
93B TYR* 1.3 77.6 - - - +
95B CYS* 1.3 61.8 + - - +
108B TRP* 4.1 11.2 - + + -
109B GLY 3.7 11.9 - - - +
110B GLN 3.4 19.3 - - - -
111B GLY* 3.5 16.6 - - - -
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Residues in contact with CYS 95 (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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4B LEU* 3.8 14.9 - - - +
6B GLU* 2.6 23.3 + - - +
22B CYS* 2.0 55.0 - - + -
34B THR* 4.9 1.1 - - + -
35B GLY 3.1 13.0 - - - +
36B TRP* 3.7 13.0 - - + +
94B TYR* 1.3 75.6 - - - +
96B GLN* 1.3 61.3 + - - +
108B TRP* 3.5 3.5 - - - -
109B GLY 3.1 23.9 + - - -
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Residues in contact with GLN 96 (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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106A GLU* 3.3 18.6 + - - -
108A TRP* 3.8 4.4 - - - -
4B LEU* 4.0 1.3 - - - -
33B THR 3.8 1.0 - - - +
34B THR* 3.4 4.9 - - - +
35B GLY* 3.0 39.3 + - - +
37B VAL* 3.2 31.7 - - + +
47B TRP* 5.5 0.6 - - - -
95B CYS* 1.3 75.6 - - - +
97B ILE* 1.3 63.2 + - - +
98B GLN* 2.9 17.5 - - + +
106B GLU* 2.6 26.8 - - - +
107B TYR 2.9 17.3 - - - +
108B TRP* 3.4 23.8 - - + +
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Residues in contact with ILE 97 (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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2B VAL* 4.4 8.7 - - + -
4B LEU* 3.6 38.4 - - + -
24B VAL* 4.4 10.5 - - + -
32B CYS* 4.6 10.3 - - + -
33B THR 3.2 4.5 - - - +
34B THR* 3.3 28.5 - - + +
96B GLN* 1.3 78.3 - - - +
98B GLN* 1.3 63.2 + - - +
99B CYS* 4.1 5.2 - - - -
105B ARG 3.7 0.5 - - - +
106B GLU* 3.0 6.2 - - - +
107B TYR* 2.9 47.9 + - + -
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Residues in contact with GLN 98 (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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96A GLN* 3.5 3.3 - - - +
98A GLN* 3.3 44.8 + - - +
106A GLU* 3.9 1.4 - - - +
32B CYS* 3.0 5.3 - - - +
33B THR* 2.9 52.6 + - - +
96B GLN* 2.9 12.8 - - + +
97B ILE* 1.3 74.4 - - - +
99B CYS* 1.3 61.0 + - - +
100B GLY 4.0 1.3 + - - -
104B ILE* 5.8 9.1 - - + +
105B ARG 3.4 7.9 - - - +
106B GLU* 2.9 38.2 - - + +
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Residues in contact with CYS 99 (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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2B VAL* 6.0 3.6 - - - -
27B SER* 5.4 6.1 - - - -
29B TYR* 3.9 25.7 - - + -
32B CYS* 2.0 49.6 - - - +
97B ILE* 4.7 11.9 - - - -
98B GLN* 1.3 75.9 - - - +
100B GLY* 1.3 57.1 + - - +
104B ILE* 5.2 0.2 - - - -
105B ARG* 3.1 31.4 + - - +
107B TYR* 4.9 11.7 - - + +
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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