Contacts of the strand formed by residues 93 - 96 (chain B) in PDB entry 4ND1
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 VAL 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS 3.3 2.7 + - - +
24B ILE* 3.4 13.6 - - + -
25B ALA 2.9 24.3 + - - -
91B SER* 3.8 2.1 - - - -
92B ASP* 1.3 81.5 - - - +
94B VAL* 1.3 69.5 + - - +
95B ILE* 3.9 26.0 - - + -
134B PHE* 3.2 14.6 - - + +
136B ILE* 4.0 17.0 - - + -
258B ALA* 4.5 7.6 - - + +
261B TYR* 3.5 30.3 - - + -
262B LEU* 4.1 20.0 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.4 9.2 - - + +
27B ILE* 3.7 28.7 - - + -
88B ILE* 4.8 0.9 - - + -
91B SER* 4.1 6.3 - - - -
93B VAL* 1.3 78.1 - - - +
95B ILE* 1.3 63.0 + - - +
96B ILE* 4.1 12.3 - - + -
127B VAL* 4.0 18.4 - - + -
131B CYS* 3.6 30.5 - - - -
133B ALA* 3.8 11.2 - - + -
134B PHE 2.8 11.1 + - - +
135B VAL* 3.3 11.6 - - + +
136B ILE 2.8 26.9 + - - +
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Residues in contact with ILE 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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24B ILE* 4.0 18.8 - - + -
25B ALA 2.8 14.0 + - - +
26B VAL* 3.4 6.5 - - - +
27B ILE 2.8 31.1 + - - -
36B ILE* 3.7 30.3 - - + -
40B VAL* 5.8 0.4 - - + -
93B VAL* 3.9 16.4 - - + -
94B VAL* 1.3 77.9 - - - +
96B ILE* 1.3 58.4 + - - +
97B THR* 3.8 1.8 + - + -
136B ILE* 3.2 16.2 - - + +
138B ILE* 3.6 30.7 - - + -
254B ALA* 4.2 25.1 - - + +
255B VAL* 5.5 0.4 - - - -
258B ALA* 4.5 6.5 - - + -
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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
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27B ILE* 3.6 6.7 - - + +
94B VAL* 4.1 11.9 - - + -
95B ILE* 1.3 75.3 - - - +
97B THR* 1.3 62.5 + - - +
98B ALA* 4.0 10.3 - - + +
120B LEU* 4.2 17.9 - - + -
123B VAL* 3.8 22.4 - - + -
135B VAL* 3.7 21.8 - - + -
136B ILE 3.0 8.6 + - - +
137B CYS* 4.4 13.0 - - + -
138B ILE* 2.9 29.0 + - - +
139B THR* 3.2 19.0 + - - +
149B PHE* 3.5 38.4 - - + -
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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