Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 5AJQ
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 LEU 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B HIS* 4.9 7.6 - - + +
82B ILE* 3.7 36.3 - - + +
85B LEU* 3.8 29.7 + - + +
86B ALA* 4.1 14.1 - - + +
94B VAL 3.9 0.8 + - - -
95B LYS* 1.3 72.5 - - - +
97B LEU* 1.3 63.3 + - - +
98B GLY* 3.6 21.3 - - - +
99B ALA* 4.3 9.9 - - + +
108B ILE* 3.8 21.8 - - + -
109B MET 3.5 15.9 - - - +
110B ILE* 3.8 6.9 - - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 4.0 33.2 - - + -
60B ALA* 5.1 8.1 - - + -
61B LEU 3.6 23.8 - - - +
62B ALA* 4.1 3.6 - - + -
95B LYS* 3.4 12.3 + - + +
96B LEU* 1.3 78.6 - - - +
98B GLY* 1.3 56.7 + - - +
100B TYR* 4.7 3.1 + - - -
109B MET* 2.8 12.9 + - - +
111B GLU* 3.7 27.1 - - + +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 5.2 0.2 - - - -
96B LEU* 3.5 10.9 - - - +
97B LEU* 1.3 79.6 - - - +
99B ALA* 1.3 59.8 + - - -
100B TYR* 4.1 13.2 - - - -
109B MET* 2.7 47.7 + - - +
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Residues in contact with ALA 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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25B HIS 3.6 19.3 + - - +
26B VAL* 3.3 11.5 - - + -
27B ARG* 2.9 23.9 + - - +
82B ILE* 3.8 32.1 - - + -
96B LEU* 4.3 6.2 - - + +
98B GLY* 1.3 74.3 - - - +
100B TYR* 1.3 66.2 - - - +
106B LEU* 5.3 0.4 - - + -
107B TRP 3.2 8.7 - - - +
108B ILE* 5.0 1.1 - - - -
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Residues in contact with TYR 100 (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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26B VAL* 3.9 4.0 - - - +
27B ARG* 3.5 24.2 - - + +
30B LEU* 4.6 17.0 - - + +
32B PRO* 3.8 35.9 - - + -
35B VAL* 3.8 23.0 - - + +
36B TRP* 3.3 38.5 + + - -
97B LEU 4.7 2.3 + - - -
98B GLY* 4.1 14.1 - - - -
99B ALA* 1.3 80.2 - - - +
101B TYR* 1.3 59.5 + - - +
102B HIS 4.1 1.1 - - - +
105B LYS 3.9 0.5 - - - +
106B LEU* 3.5 5.9 - - - +
107B TRP* 2.8 40.8 + - + +
109B MET* 3.7 18.2 - - + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.8 15.5 - - + +
27B ARG 3.2 9.2 + - - +
28B ARG* 3.4 36.3 - - + +
30B LEU 4.6 0.2 - - - +
75B LEU* 3.8 41.2 - - + +
100B TYR* 1.3 72.6 - - - +
102B HIS* 1.3 58.6 + - - +
103B ASP 3.8 15.3 + - - -
104B GLY* 3.6 27.8 + - - -
105B LYS 3.2 16.2 - - - -
106B LEU* 4.2 4.0 - - + -
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 5.3 0.2 - - - -
30B LEU 3.9 6.6 + - - +
31B ASP* 3.1 42.7 + - + +
32B PRO* 3.5 28.7 - - + -
33B ASN* 4.8 5.1 + - - -
100B TYR 4.1 0.4 - - - -
101B TYR* 1.3 75.0 - - - +
103B ASP* 1.3 96.1 + - - +
105B LYS* 3.2 24.8 + - - +
107B TRP* 4.9 5.0 + + + +
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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