Contacts of the strand formed by residues 83 - 89 (chain B) in PDB entry 4NY0
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 TYR 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.1 0.5 - - - -
68B ILE* 3.7 31.2 - - + +
72B VAL* 4.0 17.5 - - + -
77B VAL* 3.7 20.3 - - + +
79B HIS 3.3 25.1 - - - -
80B VAL* 3.3 11.4 + - - +
81B ALA 4.5 1.6 - - - +
82B CYS* 1.3 81.6 - - + +
84B GLY* 1.3 58.7 + - - +
100B VAL* 4.7 5.9 - - - +
124B LEU* 3.9 22.0 - - + -
125B ARG 3.5 7.2 - - - +
126B ILE* 3.6 23.3 - - + -
128B TYR* 3.6 11.0 - - - -
143B THR* 2.9 37.9 + - + +
146B PHE* 3.8 29.8 - + - +
349B ARG* 5.5 0.2 + - - -
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Residues in contact with GLY 84 (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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68B ILE* 3.7 10.3 - - - -
82B CYS 4.0 1.0 + - - -
83B TYR* 1.3 75.6 - - - +
85B LEU* 1.3 61.4 + - - -
97B TRP* 3.9 9.4 - - - -
98B LEU 5.7 0.7 - - - -
100B VAL* 5.6 2.9 - - - -
124B LEU* 3.6 6.9 - - - +
125B ARG* 2.9 31.6 + - - -
127B ARG 4.7 0.4 - - - +
128B TYR* 4.0 18.7 - - - -
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Residues in contact with LEU 85 (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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37B LEU* 5.2 3.6 - - + -
39B VAL* 4.1 16.4 - - + -
64B VAL* 3.7 35.0 - - + -
67B ILE* 4.6 19.5 - - + -
68B ILE* 4.1 5.7 - - + +
84B GLY* 1.3 74.1 - - - -
86B ARG* 1.3 58.3 + - - +
97B TRP* 3.7 7.0 - - - -
98B LEU* 2.9 52.3 + - + +
104B VAL* 6.2 1.3 - - + -
122B TYR* 4.4 15.9 - - + -
123B GLU 3.2 32.1 - - - +
124B LEU* 3.8 8.5 - - + +
128B TYR* 5.3 0.2 + - - -
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Residues in contact with ARG 86 (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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85B LEU* 1.3 73.1 - - - +
87B LEU* 1.3 60.7 + - - +
88B SER* 3.5 15.5 + - - +
95B VAL* 3.6 32.5 - - + +
96B HIS 3.8 2.5 - - - +
97B TRP* 3.7 40.0 - - + +
121B LYS 3.6 2.1 - - - +
122B TYR* 4.7 0.7 - - - -
123B GLU* 2.8 77.7 + - + +
125B ARG* 3.4 34.8 - - - +
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Residues in contact with LEU 87 (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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85B LEU 3.8 1.2 + - - -
86B ARG* 1.3 72.5 - - - +
88B SER* 1.3 60.7 + - - +
95B VAL* 3.5 1.9 - - - +
96B HIS* 2.8 47.8 + - + +
98B LEU* 3.8 17.0 - - + -
111B TYR* 3.8 43.1 - - + -
120B TRP* 3.7 32.3 - - + -
121B LYS 3.4 15.9 - - - +
122B TYR* 3.5 41.1 - - + +
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Residues in contact with SER 88 (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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86B ARG* 3.5 30.7 + - - +
87B LEU* 1.3 74.9 + - - +
89B HIS* 1.3 66.2 + - - +
90B LEU* 3.7 2.5 + - - -
94B GLU 3.6 4.0 - - - -
95B VAL* 3.9 16.0 - - - +
120B TRP* 3.3 7.9 - - - -
121B LYS* 3.0 41.9 + - - +
123B GLU* 5.1 3.4 + - - +
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Residues in contact with HIS 89 (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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88B SER* 1.3 75.6 - - - +
90B LEU* 1.3 63.3 + - - +
91B ARG* 3.6 24.3 - - + +
92B SER* 2.7 46.0 + - - +
94B GLU* 2.9 27.5 + - + +
115B HIS* 3.6 36.4 + + + -
119B GLU* 3.2 43.9 + - + -
120B TRP* 3.4 21.3 - + + -
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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