Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 4B92
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 ASP 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B PHE* 3.8 5.0 - - - +
70B HIS* 4.2 25.6 - - + +
79B VAL 3.7 3.2 + - - -
80B ASP* 1.3 77.6 - - - +
82B PHE* 1.3 58.9 + - - +
83B TYR* 3.5 7.9 - - - +
84B HIS* 2.7 46.5 + - - +
85B GLY* 2.9 26.7 + - - -
123B LYS* 3.7 27.6 + - + +
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Residues in contact with PHE 82 (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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69B PHE* 3.5 44.2 - + + -
70B HIS* 3.9 15.8 - + + -
81B ASP* 1.3 75.8 - - - +
83B TYR* 1.3 59.5 + - - +
85B GLY 4.1 0.2 - - - -
86B THR* 2.8 32.6 + - - +
97B ILE* 4.2 13.9 - - + -
99B GLY* 5.0 6.3 - - - -
100B HIS 5.8 1.6 - - - -
116B CYS* 3.9 25.8 - - - -
119B LEU* 3.8 18.6 + - + +
120B ALA* 3.6 43.5 - - + -
123B LYS* 4.2 7.3 - - + +
124B VAL* 3.9 14.9 - - + -
128B TYR* 4.7 6.1 - + - -
130B LEU* 4.6 7.4 - - + -
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Residues in contact with TYR 83 (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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81B ASP* 3.2 13.4 + - - +
82B PHE* 1.3 77.7 - - - +
84B HIS* 1.3 87.3 + + - +
86B THR* 3.1 3.3 + - - -
87B LYS* 2.9 51.2 + - + +
123B LYS* 3.5 32.2 + - + +
125B CYS* 3.5 28.7 - - - -
452B PHE* 3.8 16.3 - - - -
454B CYS 3.8 12.8 + - - -
456B GLU* 3.8 27.8 - - + -
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Residues in contact with HIS 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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79B VAL 5.9 1.1 - - - -
80B ASP* 3.9 20.0 - - - +
81B ASP* 2.7 38.6 + - - +
83B TYR* 1.3 95.7 - + - +
85B GLY* 1.3 56.4 - - - +
87B LYS* 3.5 16.1 + - - +
88B ALA* 2.8 31.4 + - - +
419B VAL 4.4 10.4 + - - +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.3 38.8 - - - -
80B ASP* 4.0 6.2 - - - +
81B ASP 2.9 14.3 + - - -
84B HIS* 1.3 76.3 - - - +
86B THR* 1.3 57.4 + - - +
88B ALA* 3.2 7.5 + - - +
89B ALA* 2.9 25.1 + - - +
351B VAL* 4.1 1.4 - - - +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.7 4.7 - - + -
82B PHE 2.8 23.7 + - - +
83B TYR 3.1 8.0 + - - -
85B GLY* 1.3 75.5 - - - +
87B LYS* 1.3 63.2 + - - +
89B ALA* 3.1 10.1 + - - +
90B LEU* 3.0 28.2 + - - +
97B ILE* 4.0 18.2 - - + -
124B VAL* 4.0 13.9 - - + -
125B CYS* 2.8 32.1 + - - +
126B CYS* 3.7 23.1 - - - +
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Residues in contact with LYS 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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83B TYR* 2.9 38.5 + - + +
84B HIS* 3.5 16.6 + - - +
86B THR* 1.3 77.4 + - - +
88B ALA* 1.3 64.3 + - - +
90B LEU* 3.1 4.0 + - - +
91B VAL* 3.1 26.9 + - + +
125B CYS* 4.3 1.7 - - - -
419B VAL* 4.5 26.0 - - + +
452B PHE* 3.7 59.8 - - + +
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Residues in contact with ALA 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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80B ASP* 4.9 0.2 - - - +
84B HIS 2.8 19.3 + - - +
85B GLY* 3.2 6.0 + - - +
87B LYS* 1.3 76.8 - - - +
89B ALA* 1.3 61.8 + - - +
91B VAL* 3.7 0.5 + - - +
92B GLY 3.2 14.7 + - - -
351B VAL* 3.4 20.9 - - + -
352B GLN* 3.2 16.9 - - + +
419B VAL* 3.7 16.4 - - + +
420B GLN* 3.8 25.4 - - + -
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Residues in contact with ALA 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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85B GLY 2.9 12.4 + - - +
86B THR* 3.2 11.4 - - - +
88B ALA* 1.3 77.1 - - - +
90B LEU* 1.3 54.2 + - - +
92B GLY* 2.8 22.0 + - - -
93B GLY 2.9 0.5 + - - -
94B THR* 2.8 48.2 + - + +
97B ILE* 4.0 11.2 - - + -
126B CYS* 4.9 1.1 - - - -
351B VAL* 3.9 20.3 - - + +
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Residues in contact with LEU 90 (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 THR 3.0 15.3 + - - +
87B LYS 3.1 4.9 + - - +
89B ALA* 1.3 72.2 - - - +
91B VAL* 1.3 65.2 + - - +
93B GLY 3.0 6.2 + - - -
94B THR 3.3 17.0 - - - +
95B THR* 3.9 6.1 - - - -
125B CYS* 3.5 40.2 - - + +
126B CYS* 3.7 17.9 - - + -
439B THR* 2.7 44.9 + - + +
441B SER* 4.0 7.4 - - - -
446B VAL* 3.9 24.2 - - + -
447B TYR* 4.8 1.1 - - - -
452B PHE* 3.9 17.5 - - + -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.1 18.6 + - + +
88B ALA 4.1 4.7 - - - +
90B LEU* 1.3 75.9 - - - +
92B GLY* 1.3 56.2 + - - +
93B GLY 3.3 0.2 - - - -
352B GLN* 3.6 20.8 + - - +
411B LYS* 5.6 4.0 - - - +
419B VAL* 4.2 20.6 - - + -
436B PRO* 3.3 19.6 - - - +
447B TYR* 3.6 50.1 - - + +
452B PHE* 3.9 18.2 - - + -
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Residues in contact with GLY 92 (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 ALA 3.2 9.8 + - - -
89B ALA 2.8 13.1 + - - -
91B VAL* 1.3 77.6 - - - +
93B GLY* 1.3 53.6 + - - -
94B THR* 3.4 1.5 + - - -
351B VAL 5.3 1.0 - - - +
352B GLN* 3.4 29.1 - - - +
355B MET* 3.3 27.0 + - - +
356B SER* 4.9 1.2 + - - -
405B TRP* 4.5 0.5 - - - -
436B PRO* 3.9 8.8 - - - +
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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