Contacts of the strand formed by residues 174 - 181 (chain A) in PDB entry 4FO9
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 PHE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLN* 4.0 14.1 - - - +
173A ARG* 1.3 88.7 - - + +
175A GLN* 1.3 65.2 + - - +
229A SER* 4.0 21.1 - - - -
280A SER* 6.0 2.5 - - - -
281A TRP 3.5 15.3 - - - -
282A ALA* 3.7 20.6 - - + -
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Residues in contact with GLN 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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167A VAL 4.1 2.6 - - - +
168A GLN* 3.4 12.4 - - + +
169A SER* 3.0 42.7 + - - +
172A GLN 3.0 26.5 + - - -
173A ARG 3.4 12.0 + - - +
174A PHE* 1.3 77.4 + - - +
176A GLU* 1.3 62.8 + - - +
177A LYS* 5.6 0.2 - - + -
280A SER* 3.2 25.5 - - - -
281A TRP* 2.8 52.6 + - + +
283A SER* 3.8 4.0 + - - +
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Residues in contact with GLU 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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175A GLN* 1.3 76.6 - - - +
177A LYS* 1.3 74.0 + - - +
178A PHE* 3.2 39.4 - - + -
233A LYS* 5.5 5.4 + - - +
278A SER* 4.0 11.3 - - - -
279A ILE 3.3 9.4 - - - +
280A SER* 3.4 21.1 + - - +
281A TRP* 4.2 0.2 - - - -
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Residues in contact with LYS 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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166A LEU* 4.8 3.4 - - + -
167A VAL* 4.4 13.0 - - + +
176A GLU* 1.3 80.8 - - - +
178A PHE* 1.3 66.0 + - - +
179A PHE* 3.8 24.5 - - + -
278A SER* 3.4 2.4 - - - -
279A ILE 2.8 33.4 + - - -
281A TRP* 3.5 28.9 - - + -
513A UNX 3.6 8.3 - - - -
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Residues in contact with PHE 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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176A GLU* 3.2 37.2 - - + -
177A LYS* 1.3 74.0 - - - +
179A PHE* 1.3 71.7 - - - +
180A ILE* 5.9 1.1 - - + -
276A GLN* 3.7 25.6 - - + +
277A ILE 3.3 3.4 - - - -
278A SER* 2.8 35.4 - - - -
503A UNX 4.2 4.7 - - - -
513A UNX 3.1 21.3 - - - -
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Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.8 26.0 - - + -
164A THR* 3.8 28.3 - - + -
165A SER 5.3 0.9 - - - -
166A LEU* 3.7 22.7 - - + -
177A LYS* 3.8 29.6 - - + -
178A PHE* 1.3 75.6 - - - +
180A ILE* 1.3 64.4 + - - +
181A PHE 4.3 0.2 + - - -
275A ASN 4.0 0.2 - - - +
276A GLN* 3.4 4.3 - - - +
277A ILE* 2.7 50.5 + - + +
279A ILE* 3.9 15.0 - - + -
291A MET* 3.6 32.8 - - + -
503A UNX 3.5 10.5 - - - -
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Residues in contact with ILE 180 (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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160A LEU 5.3 0.2 - - - +
161A ILE* 4.2 10.7 - - - +
178A PHE* 5.9 1.6 - - + -
179A PHE* 1.3 82.2 - - - +
181A PHE* 1.3 67.5 + - - +
182A ALA* 5.6 1.1 - - + -
274A PRO* 3.7 30.5 - - + -
275A ASN 3.4 10.3 - - - +
276A GLN* 3.6 22.2 - - + +
503A UNX 3.2 16.6 - - - -
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Residues in contact with PHE 181 (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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160A LEU* 4.0 34.5 - - + +
161A ILE* 4.1 17.9 - - + -
179A PHE 5.4 0.2 - - - -
180A ILE* 1.3 76.7 - - - +
182A ALA* 1.3 62.5 + - - +
183A LEU* 4.0 26.0 - - + -
209A VAL* 4.1 20.4 - - + -
234A VAL* 5.9 0.9 - - + -
263A ILE* 5.1 0.7 - - + -
267A VAL* 4.2 9.6 - - + -
274A PRO* 3.5 3.6 - - - +
275A ASN* 2.7 70.0 + - + +
277A ILE* 3.8 26.9 - - + -
293A VAL* 4.6 5.6 - - + -
515A UNX 3.7 15.0 - - - -
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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