Contacts of the strand formed by residues 96 - 103 (chain B) in PDB entry 4AY1
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 LYS 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER 3.1 10.1 + - - +
58B HIS* 3.2 36.3 - - + +
59B LEU 2.8 25.6 + - - -
93B PRO 5.3 2.0 + - - -
94B LYS* 3.9 18.3 + - - +
95B LEU* 1.3 77.7 - - - +
97B ILE* 1.3 66.3 + - - +
98B LEU* 4.2 6.7 - - + -
138B ASP* 3.4 26.9 + - + +
176B GLU* 3.8 22.8 + - - -
179B LEU* 4.6 13.0 - - + -
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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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33B PHE* 5.3 8.3 - - + -
59B LEU* 3.4 33.9 - - + +
61B TYR 5.4 0.2 - - - +
85B ILE* 4.2 26.0 - - + +
88B LEU* 4.3 10.3 - - + -
89B LYS* 3.8 30.5 - - + -
95B LEU* 3.9 14.6 - - + -
96B LYS* 1.3 79.9 - - - +
98B LEU* 1.3 62.0 + - - +
136B ASN 5.0 0.2 - - - +
137B PHE* 3.3 28.1 - - + -
138B ASP* 2.7 41.7 + - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B HIS* 4.1 28.3 - - + -
59B LEU 2.9 14.7 + - - +
60B ILE* 3.5 18.3 - - + -
61B TYR* 3.1 22.9 + - - +
96B LYS* 4.3 10.1 - - + -
97B ILE* 1.3 80.7 - - - +
99B LEU* 1.3 61.4 + - - +
137B PHE* 3.6 9.0 - - - -
138B ASP* 4.7 0.9 - - + -
139B GLY* 3.3 29.2 - - - +
140B LEU 4.3 4.9 - - - +
141B ASP 4.7 0.4 - - - +
179B LEU* 4.4 14.8 - - + -
181B THR* 3.6 37.5 - - + +
206B PHE* 5.1 1.8 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 4.5 0.2 - - - -
61B TYR* 3.5 31.4 - - + -
64B ALA* 3.6 31.0 - - + -
71B VAL* 3.8 18.4 - - + -
73B ILE* 3.9 12.8 - - + -
98B LEU* 1.3 73.3 - - - +
100B SER* 1.3 60.3 + - - +
128B ILE* 5.3 0.7 - - + -
131B PHE* 3.9 22.0 - - + -
132B LEU* 4.0 16.2 - - + -
137B PHE* 3.7 18.7 - - + -
139B GLY 3.0 7.1 + - - -
140B LEU* 3.3 15.0 - - + +
141B ASP* 2.8 24.8 + - - -
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Residues in contact with SER 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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32B TYR* 4.1 1.7 - - - -
60B ILE* 3.5 19.7 - - - +
61B TYR 2.8 19.1 + - - +
63B PHE* 3.3 29.8 - - - -
64B ALA* 2.8 31.9 + - - +
99B LEU* 1.3 73.9 - - - +
101B ILE* 1.3 60.2 + - - +
141B ASP* 2.9 24.5 + - - -
143B SER* 3.8 2.9 + - - -
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Residues in contact with ILE 101 (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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64B ALA* 3.8 24.7 - - + +
65B SER 4.5 0.4 - - - +
66B ILE* 4.3 9.4 - - + -
71B VAL* 3.8 23.6 - - + -
99B LEU* 4.9 0.7 - - + -
100B SER* 1.3 80.2 - - - +
102B GLY* 1.3 62.5 + - - +
106B PHE* 4.0 23.8 - - + -
111B PHE* 4.2 15.0 - - + -
124B PHE* 3.7 31.4 - - + -
128B ILE* 4.1 6.3 - - + -
140B LEU* 4.0 12.3 - - + -
141B ASP 2.8 8.5 + - - +
142B VAL* 3.6 7.2 - - + -
143B SER 2.8 24.9 + - - -
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Residues in contact with GLY 102 (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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63B PHE* 3.4 25.0 - - - +
64B ALA 4.4 2.0 + - - -
101B ILE* 1.3 80.7 - - - +
103B GLY* 1.3 62.7 + - - -
106B PHE* 3.1 35.3 + - - +
111B PHE* 4.1 5.2 - - - -
143B SER 3.2 8.5 - - - -
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Residues in contact with GLY 103 (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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63B PHE* 3.5 26.7 - - - -
102B GLY* 1.3 74.8 - - - -
104B TYR* 1.3 66.3 + - - -
105B LEU 3.5 1.6 - - - -
106B PHE 3.5 0.3 + - - -
107B GLY 3.2 16.8 + - - -
143B SER* 2.7 15.4 + - - -
145B ILE* 3.5 20.8 + - - +
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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