Contacts of the strand formed by residues 95 - 99 (chain B) in PDB entry 4LT6
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 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 4.3 13.2 - - - +
71B VAL* 4.5 5.1 - - - +
94B GLY* 1.3 75.8 - - - +
96B ILE* 1.3 80.4 + - - +
97B PHE* 3.0 49.7 - - + +
116B LEU 3.9 0.5 - - - +
117B CYS* 3.8 1.7 - - - -
118B VAL* 3.1 34.5 + - - +
177B ILE* 4.1 9.4 - - + +
178B SER 4.3 7.9 - - - +
179B ASP* 3.6 28.2 + - - +
180B ASN* 4.9 1.4 - - - +
181B LEU* 4.3 4.4 + - + +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.7 11.2 - - + +
67B LEU* 3.8 22.0 - - + -
68B ASN* 3.4 43.4 + - + +
71B VAL* 3.6 25.8 - - + -
95B LYS* 1.3 91.6 - - - +
97B PHE* 1.3 72.2 + - - +
98B THR* 4.4 2.1 + - + +
115B ALA* 4.2 15.0 - - + -
116B LEU 3.4 3.8 - - - +
117B CYS* 3.8 21.1 - - + -
167B LEU* 4.0 5.8 - - + -
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Residues in contact with PHE 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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95B LYS* 3.0 55.4 - - + +
96B ILE* 1.3 79.2 - - - +
98B THR* 1.3 64.1 + - - +
115B ALA* 3.4 2.4 - - - -
116B LEU* 2.7 46.3 + - + +
118B VAL* 4.0 26.2 - - + -
181B LEU* 3.4 30.1 - - + -
183B LEU* 3.8 28.9 - - + -
203B CYS* 3.5 20.6 - - + -
207B ASP* 5.4 4.9 - - - -
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.5 36.1 - - + -
96B ILE* 5.3 1.8 - - + -
97B PHE* 1.3 78.2 - - - +
99B PHE* 1.3 63.6 + - - +
102B TYR* 3.8 16.7 - - + -
103B ARG* 3.4 39.9 + - - +
113B ILE* 3.7 17.0 - - + -
114B ASP 3.4 5.8 - - - -
115B ALA* 5.1 2.0 - - + -
203B CYS* 3.9 5.9 - - - -
206B THR* 5.5 0.2 - - - -
207B ASP* 5.2 1.4 - - - +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 1.3 75.9 - - - +
100B GLY* 1.3 69.8 + - - +
101B SER 3.8 0.7 + - - -
102B TYR* 4.4 1.4 + - - +
103B ARG* 3.4 13.8 + - - -
114B ASP* 2.8 54.4 + - + +
115B ALA 3.7 18.4 - - - -
116B LEU* 4.0 5.8 - - + -
166B ASP 5.3 1.1 - - - -
168B VAL* 4.9 15.9 - - + -
199B SER 5.5 2.2 - - - -
202B GLY* 3.7 39.0 - - - +
203B CYS* 3.7 26.2 - - - +
206B THR* 3.7 4.0 - - - +
601B 3AT 3.4 34.5 - + - -
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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