Contacts of the strand formed by residues 170 - 176 (chain B) in PDB entry 5FJV
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 ASN 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B CYS* 3.4 14.1 - - - -
158B SER* 4.3 9.5 + - - -
169B GLN* 1.3 74.0 - - - +
171B CYS* 1.3 58.9 + - - +
172B LYS* 4.0 11.1 + - - +
232B ALA* 4.0 22.3 - - - +
233B PHE 3.3 12.6 - - - +
234B VAL* 4.6 6.0 - - + +
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Residues in contact with CYS 171 (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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72B VAL* 5.5 5.2 - - - -
79B MET* 3.1 39.7 - - + -
157B CYS* 2.0 43.5 - - - -
169B GLN* 3.8 12.9 + - - -
170B ASN* 1.3 72.6 - - - +
172B LYS* 1.3 60.1 + - - +
232B ALA* 4.8 0.7 - - - -
233B PHE* 3.0 43.4 + - + -
235B ILE* 4.8 11.0 - - + -
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Residues in contact with LYS 172 (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 MET* 4.7 3.3 - - - +
122B TYR* 6.0 0.2 - - - +
123B ASN* 3.5 31.4 + - - +
157B CYS* 4.3 17.5 + - - +
170B ASN* 4.0 11.5 + - - +
171B CYS* 1.3 75.3 - - - +
173B MET* 1.3 63.8 + - - +
174B LYS* 4.3 12.1 - - + +
230B THR* 3.9 21.1 - - + -
231B TYR 3.0 10.5 - - - +
232B ALA* 4.5 5.6 - - + +
68C GLN* 4.0 5.9 + - - -
201C GLU* 2.5 46.7 + - - -
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Residues in contact with MET 173 (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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64B LEU* 4.6 7.2 - - - -
66B ILE* 5.7 0.2 - - - -
79B MET* 4.6 7.2 - - + -
81B THR* 3.9 21.5 - - - +
83B VAL* 4.7 4.5 - - + -
121B LEU* 4.1 9.4 - - + -
123B ASN* 3.9 2.9 - - - -
153B TYR* 3.9 30.7 - - + -
155B SER* 4.0 13.9 - - - +
172B LYS* 1.3 77.6 - - - +
174B LYS* 1.3 60.7 + - - +
175B PHE* 3.5 35.2 - - + -
230B THR* 3.1 3.6 - - - -
231B TYR* 2.7 43.7 + - + -
233B PHE* 3.9 28.0 - - + -
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Residues in contact with LYS 174 (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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121B LEU* 3.7 3.6 - - - +
122B TYR* 2.9 73.5 + - + +
123B ASN* 3.5 13.1 + - - +
172B LYS* 4.2 7.6 - - + +
173B MET* 1.3 70.8 - - - +
175B PHE* 1.3 61.3 + - - +
219B TYR* 3.1 32.6 + - - -
228B ASP* 3.6 23.3 - - + +
230B THR* 3.5 24.5 - - + +
84C TRP* 5.2 1.6 - - - -
199C TYR* 5.9 1.2 - - - +
201C GLU* 4.6 17.0 + - - +
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Residues in contact with PHE 175 (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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62B PHE* 3.3 34.1 - + + -
64B LEU* 4.4 17.7 - - + -
85B LEU* 3.9 17.5 - - + -
119B ILE* 4.0 8.3 - - + -
120B VAL 3.6 12.6 - - - -
121B LEU* 4.2 11.0 - - + -
122B TYR* 4.3 1.1 - - - -
153B TYR* 3.9 31.4 - + - -
173B MET* 3.5 43.1 - - + -
174B LYS* 1.3 74.8 - - - +
176B GLY* 1.3 58.1 + - - +
187B LEU* 5.8 0.4 - - - +
228B ASP* 3.1 7.9 - - - +
229B VAL 2.9 33.2 + - - +
231B TYR* 4.0 20.0 - + - -
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Residues in contact with GLY 176 (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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119B ILE* 3.6 13.9 - - - +
120B VAL* 3.1 29.0 + - - +
122B TYR* 3.8 14.5 - - - -
175B PHE* 1.3 76.1 - - - +
177B SER* 1.3 68.0 + - - -
178B TRP 3.5 0.3 + - - -
187B LEU* 4.6 4.0 - - - -
227B PRO 4.1 12.8 - - - -
228B ASP* 4.5 1.1 - - - -
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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