Contacts of the strand formed by residues 172 - 179 (chain A) in PDB entry 2FK8
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 ARG 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP 5.4 0.2 + - - -
68A LYS 2.9 28.6 + - - +
69A LEU* 3.7 23.3 - - + +
70A ASP* 3.5 23.0 + - - +
141A ARG* 3.5 15.3 - - - +
142A ILE 3.1 20.4 + - - -
167A MET* 3.2 9.7 - - - +
170A ASP 3.7 7.2 + - - +
171A GLY* 1.3 81.2 - - - +
173A MET* 1.3 62.1 + - - +
293A THR* 5.4 0.7 - - + -
294A TYR 3.3 9.2 - - - +
295A LEU* 3.6 26.6 - - + +
299A ALA* 4.1 8.4 - - + +
300A ALA* 2.9 41.6 + - - +
301A ALA 4.6 4.8 + - - -
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.8 1.1 - - - -
142A ILE* 3.0 32.1 - - + +
144A SER* 5.5 0.4 - - - -
159A PHE* 4.0 5.6 - - + -
160A PHE* 3.9 26.9 - - + -
163A CYS* 3.5 43.5 - - + -
167A MET* 4.0 7.2 - - + -
172A ARG* 1.3 78.4 - - - +
174A THR* 1.3 77.3 + - - +
175A VAL* 4.0 10.1 - - + -
229A PHE* 4.1 10.1 - - + -
293A THR* 3.5 4.5 - - - +
294A TYR* 2.8 48.6 + - + -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASN* 3.0 33.2 + - - +
68A LYS* 3.7 35.2 - - + -
69A LEU* 3.7 8.1 - - + +
142A ILE 3.0 7.3 + - - -
143A VAL* 3.6 15.2 - - - +
144A SER 2.9 25.3 + - - -
173A MET* 1.3 82.2 - - - +
175A VAL* 1.3 65.7 + - - +
176A GLN 4.2 0.4 - - - -
291A LEU* 3.8 6.5 - - + -
292A VAL 3.3 2.9 - - - -
293A THR* 4.0 13.7 - - + +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A SER* 3.3 14.4 - - - +
148A PHE* 3.8 34.8 - - + -
159A PHE* 4.3 13.0 - - + -
160A PHE* 4.6 0.9 - - + -
173A MET* 4.0 18.6 - - + -
174A THR* 1.3 79.0 - - - +
176A GLN* 1.3 63.1 + - - +
220A MET* 3.8 16.7 - - + +
290A SER 3.5 2.6 - - - +
291A LEU* 4.4 1.6 - - - -
292A VAL* 2.8 33.9 + - - -
294A TYR* 3.3 29.6 - - + -
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A CYS* 3.5 26.7 + - - +
61A LYS* 3.5 9.2 - - - +
65A ASN* 3.1 32.0 + - - +
144A SER 2.9 8.7 + - - +
145A ILE* 3.8 23.1 - - + +
146A GLU* 2.8 54.2 + - + +
147A ALA 4.7 0.3 + - - -
148A PHE* 5.0 0.3 - - - +
174A THR 4.2 0.2 - - - -
175A VAL* 1.3 75.2 - - - +
177A SER* 1.3 65.0 + - - +
237A LEU* 3.6 24.0 - - + +
289A CYS* 4.1 3.4 - - - -
290A SER 3.3 7.0 - - - +
291A LEU* 4.1 6.3 - - + +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLU* 4.3 1.3 - - - -
148A PHE* 4.0 12.1 - - - +
149A GLU* 3.1 25.0 + - - +
175A VAL 4.1 0.2 + - - -
176A GLN* 1.3 77.5 - - - +
178A SER* 1.3 80.9 + - - +
179A VAL* 3.8 2.9 - - - +
215A PRO* 3.8 8.3 - - - +
220A MET* 3.8 23.8 - - - -
289A CYS* 4.0 5.8 - - - -
290A SER 2.9 32.7 + - - +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLU* 4.2 2.5 + - - +
149A GLU* 2.9 20.2 + - - +
177A SER* 1.3 86.1 + - - +
179A VAL* 1.3 61.4 + - - +
214A LEU* 3.9 19.5 - - - +
215A PRO* 3.4 11.1 - - - +
241A TYR* 3.6 24.6 + - - -
274A TYR* 5.8 0.5 + - - -
282A PHE* 4.0 9.7 - - - -
287A LEU* 6.3 1.6 - - - -
288A ASP 3.4 10.5 - - - -
289A CYS* 4.1 4.2 - - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER 3.8 5.2 - - - +
178A SER* 1.3 81.7 - - - +
180A SER* 1.3 62.8 + - - +
181A TYR* 5.6 2.5 - - + -
214A LEU* 4.4 6.5 - - - +
215A PRO* 3.2 12.8 - - + +
216A SER 3.8 0.4 - - - -
217A THR* 3.4 41.3 - - - +
220A MET* 3.6 24.7 - - - -
287A LEU* 3.6 10.7 - - - +
288A ASP* 2.9 58.8 + - + +
290A SER* 3.9 4.7 - - - +
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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