Contacts of the strand formed by residues 85 - 92 (chain B) in PDB entry 3N56
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 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B THR* 2.7 25.9 + - - +
84B ASP* 1.3 81.9 - - + +
86B SER* 1.3 62.3 - - - +
135B ALA* 3.7 21.9 + - - +
137B SER* 6.1 0.4 - - - -
152B ASP* 3.3 40.2 + - - +
153B VAL 3.2 12.8 - - - +
154B SER* 4.9 1.8 - - - +
155B HIS* 4.3 0.2 - - - -
259B LEU* 4.3 0.3 - - - +
430B PRO* 3.9 18.4 - - + +
891B ILE* 5.0 7.4 - - + -
892B ARG* 4.7 22.5 - - - +
895B ASP* 3.3 30.1 + - - +
898B LYS* 5.8 2.1 - - - +
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Residues in contact with SER 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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83B THR* 4.4 0.3 - - - +
85B LYS* 1.3 75.4 + - - +
87B SER* 1.3 65.2 + - - +
152B ASP* 3.6 3.8 - - - +
153B VAL* 2.7 37.9 + - - +
155B HIS* 3.3 30.6 + - - +
158B LEU* 3.7 22.2 - - - +
259B LEU* 3.3 11.4 - - - -
260B GLY* 3.3 19.1 - - - -
261B ARG 4.0 0.7 + - - -
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Residues in contact with SER 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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86B SER* 1.3 78.4 - - - +
88B ALA* 1.3 60.9 + - - +
151B PHE* 2.6 26.3 + - - -
152B ASP* 4.8 1.1 - - - -
158B LEU* 4.5 2.7 - - - +
258B VAL* 3.6 2.8 - - - +
259B LEU* 2.8 36.0 + - - +
430B PRO* 3.7 27.8 - - - -
431B ARG* 3.2 11.8 - - - -
434B THR* 3.1 21.4 + - - +
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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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87B SER* 1.3 77.3 + - - +
89B ALA* 1.3 62.2 - - - +
150B TYR* 3.3 2.8 - - - +
151B PHE* 3.1 57.3 + - + +
158B LEU* 5.0 0.2 - - + -
162B LEU* 3.6 19.3 - - + -
165B PHE* 4.6 4.2 - - + -
256B VAL* 5.3 0.9 - - + -
257B VAL 3.1 12.3 - - - +
258B VAL* 4.0 8.3 - - + -
434B THR* 3.9 4.3 + - - -
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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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88B ALA* 1.3 75.9 - - - +
90B LEU* 1.3 60.2 + - - +
148B ASN* 4.6 0.9 - - - +
149B TYR 3.0 14.1 - - - +
150B TYR* 3.9 2.9 - - + +
165B PHE* 4.2 3.4 - - - -
256B VAL* 3.2 7.9 - - - +
257B VAL 2.9 31.1 + - - +
434B THR* 3.5 34.5 - - - +
435B SER* 3.6 12.6 - - - +
438B ALA* 4.0 6.3 - - + +
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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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73B ILE* 5.8 1.6 - - + -
89B ALA* 1.3 74.6 - - - +
91B ASP* 1.3 63.7 + - - +
92B VAL* 3.5 29.4 - - + -
147B THR 3.8 1.6 - - - +
148B ASN* 3.4 1.6 - - - -
149B TYR* 2.8 35.1 + - - +
165B PHE* 3.7 9.0 - - + -
169B PHE* 3.6 46.4 - - + -
254B MET* 3.9 25.1 - - + -
255B ALA 3.3 12.1 - - - +
256B VAL* 4.4 8.5 - - + -
275B PHE* 3.9 23.8 - - + -
438B ALA* 4.3 2.0 - - - -
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Residues in contact with ASP 91 (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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90B LEU* 1.3 74.9 - - - +
92B VAL* 1.3 61.2 + - - +
141B PHE* 5.5 0.5 - - - -
146B HIS* 2.7 45.6 - - - +
147B THR 3.4 4.5 - - - -
148B ASN* 3.0 24.8 + - - +
254B MET* 3.5 1.7 - - - -
255B ALA 2.8 33.0 + - - -
438B ALA 3.4 24.5 - - - +
439B GLY* 3.7 11.7 - - - -
442B HIS* 3.0 19.4 - - - -
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Residues in contact with VAL 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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90B LEU* 3.5 23.1 - - + -
91B ASP* 1.3 74.4 - - - +
93B HIS* 1.3 57.6 - - - +
94B ILE* 2.7 29.2 + - + +
146B HIS* 3.3 3.6 - - - -
147B THR* 2.9 35.8 + - - +
149B TYR* 4.7 0.7 - - + -
169B PHE* 4.4 2.2 - - + -
248B TYR 4.0 20.6 - - - +
249B TYR* 3.7 39.3 - - + -
250B SER 5.0 0.2 - - - +
253B LEU* 3.3 13.7 - - + +
254B MET* 4.1 10.3 - - + -
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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