Contacts of the strand formed by residues 172 - 177 (chain D) 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 LYS 172 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASN* 2.4 35.2 + - - +
155D SER* 3.2 7.3 + - - -
156D SER 3.9 5.2 + - - +
170D ASN* 4.7 18.2 - - - +
171D CYS* 1.3 75.0 - - - +
173D MET* 1.3 56.0 + - - +
174D LYS* 3.4 31.5 - - - +
230D THR* 3.7 17.6 + - + +
231D TYR 3.5 9.6 - - - +
232D ALA* 4.4 10.8 - - + +
201E GLU* 2.5 46.7 + - - +
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Residues in contact with MET 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU* 4.2 14.6 - - + -
79D MET* 4.4 5.6 - - + -
81D THR* 3.4 29.4 - - - +
83D VAL* 4.8 5.8 - - + -
121D LEU* 4.3 5.6 - - + -
123D ASN* 3.6 3.6 - - - +
153D TYR* 3.6 33.9 - - + -
155D SER* 4.0 17.7 - - - +
172D LYS* 1.3 79.7 - - - +
174D LYS* 1.3 60.3 + - - +
175D PHE* 3.6 31.0 - - + -
230D THR* 3.4 4.4 - - - -
231D TYR* 2.8 33.3 + - - +
233D PHE* 4.2 20.0 - - + -
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.4 9.6 - - - +
122D TYR* 2.6 67.9 + - + +
123D ASN* 3.9 7.3 - - + +
172D LYS* 3.4 26.8 - - - +
173D MET* 1.3 69.1 - - - +
175D PHE* 1.3 57.4 + - - +
217D LYS* 3.2 23.0 - - - +
219D TYR* 3.4 20.9 + - - -
228D ASP* 2.8 43.4 + - - +
229D VAL 4.1 0.9 - - - -
230D THR* 3.8 11.2 + - - +
199E TYR* 5.4 4.3 - - - -
201E GLU* 4.4 6.7 + - - +
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Residues in contact with PHE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 3.4 31.5 - + + -
64D LEU* 3.9 17.9 - - + -
83D VAL* 5.1 1.3 - - + -
85D LEU* 3.8 20.6 - - + -
119D ILE* 4.2 6.7 - - + -
120D VAL 3.4 13.0 - - - -
121D LEU* 3.8 16.6 - - + -
122D TYR* 4.0 4.3 - - - -
153D TYR* 3.6 40.2 - + - -
173D MET* 3.6 38.6 - - + -
174D LYS* 1.3 73.9 - - - +
176D GLY* 1.3 57.7 + - - +
187D LEU* 5.2 0.3 - - - +
228D ASP* 3.1 7.8 - - - +
229D VAL* 3.0 36.0 + - - +
231D TYR* 4.2 5.4 - + - -
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Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 2.8 13.6 - - - +
120D VAL* 2.5 44.2 + - - +
122D TYR* 3.6 13.2 - - - -
175D PHE* 1.3 76.2 - - - +
177D SER* 1.3 66.3 + - - -
178D TRP 3.4 0.2 + - - -
187D LEU* 4.9 5.2 - - - -
227D PRO 4.4 8.5 - - - -
228D ASP* 4.7 0.2 - - - -
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP* 2.9 18.0 + - - -
119D ILE* 3.9 11.1 - - - +
120D VAL* 4.9 0.2 - - - -
122D TYR* 3.3 16.3 + - - -
176D GLY* 1.3 73.1 - - - -
178D TRP* 1.3 59.8 + - - +
180D TYR* 2.8 44.8 + - - +
185D ILE* 3.7 22.7 - - - -
187D LEU* 4.9 6.5 - - - +
226D TYR* 4.5 3.6 - - - +
227D PRO* 4.6 7.6 + - - +
300D EPJ 4.3 1.4 + - - -
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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