Contacts of the strand formed by residues 176 - 184 (chain A) in PDB entry 4D85
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 TYR 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ILE* 4.1 2.9 - - + -
172A ASP 4.0 1.8 - - - -
173A HIS* 2.9 68.9 - + + +
174A SER 3.4 2.1 - - - -
175A LEU* 1.3 80.9 - - - +
177A THR* 1.3 72.9 + - - +
178A GLY 3.5 17.5 - - - -
179A SER* 4.6 0.4 - - - -
180A LEU* 4.3 22.0 - - + +
329A TYR* 3.4 34.5 - + + -
342A ALA* 3.5 28.5 - - + -
343A VAL 3.1 16.6 - - - +
345A ALA* 3.9 3.4 - - - +
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Residues in contact with THR 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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176A TYR* 1.3 85.5 - - - +
178A GLY* 1.3 69.6 + - - +
179A SER 3.7 0.9 + - - -
342A ALA* 4.1 0.2 - - - +
343A VAL* 3.0 42.9 + - - +
344A SER 5.0 0.5 + - - -
345A ALA* 5.0 13.2 - - + -
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Residues in contact with GLY 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 TYR* 3.5 13.7 - - - -
177A THR* 1.3 79.3 - - - +
179A SER* 1.3 59.1 + - - -
343A VAL* 5.9 1.1 - - - -
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Residues in contact with SER 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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176A TYR* 4.6 1.8 - - - -
177A THR 3.7 0.5 + - - +
178A GLY* 1.3 74.7 - - - -
180A LEU* 1.3 78.5 + - - +
181A TRP* 3.8 20.5 + - - +
341A PHE 3.6 3.3 - - - +
342A ALA* 3.5 17.8 - - - +
343A VAL 4.8 0.2 + - - -
357A VAL* 4.7 4.8 + - - +
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Residues in contact with LEU 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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171A ILE* 3.9 21.3 - - + -
173A HIS* 5.9 0.2 - - + -
176A TYR* 4.3 24.4 - - + +
179A SER* 1.3 86.2 + - - +
181A TRP* 1.3 63.6 + - - +
182A TYR* 3.6 37.5 - - + +
329A TYR* 4.2 6.1 - - + +
331A VAL* 3.9 19.7 - - + -
340A GLY* 4.0 1.6 - - - -
341A PHE 3.3 20.4 - - - +
342A ALA* 3.4 24.2 - - + +
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Residues in contact with TRP 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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179A SER* 3.8 18.1 + - - +
180A LEU* 1.3 79.6 + - - +
182A TYR* 1.3 63.4 + - - +
286A GLN* 3.6 24.7 - - - -
288A PHE* 3.3 44.7 - + + -
339A ILE 3.6 0.3 - - - +
340A GLY* 3.3 0.7 - - - -
341A PHE 2.8 36.0 + - - -
357A VAL* 3.4 35.4 + - + -
358A GLU* 4.6 0.2 - - - +
359A GLY 3.3 38.3 - - - +
360A PRO* 3.4 18.2 - - + -
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Residues in contact with TYR 182 (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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171A ILE* 4.0 12.6 - - - +
180A LEU* 3.6 41.7 - - + +
181A TRP* 1.3 78.1 - - - +
183A THR* 1.3 59.0 + - - +
281A GLY* 3.7 0.5 - - - -
282A GLU* 3.5 47.5 + - + +
286A GLN* 5.5 0.2 + - - -
288A PHE* 3.2 12.8 - - - -
331A VAL* 4.6 4.2 - - + +
333A ASP* 4.3 12.7 + - + -
336A ARG* 5.3 1.9 + - - -
338A ARG* 3.2 61.2 + - + -
339A ILE 3.1 3.8 - - - +
340A GLY* 3.6 24.2 - - - -
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Residues in contact with THR 183 (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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182A TYR* 1.3 75.3 - - - +
184A PRO* 1.3 68.6 + - - +
193A VAL* 3.9 29.1 - - + +
194A ILE 4.4 1.9 + - - -
279A LEU* 3.8 21.4 - - + +
280A MET* 2.7 24.5 + - - +
282A GLU* 5.9 0.2 - - - -
288A PHE* 3.8 3.5 - - - -
338A ARG* 3.4 3.6 - - - -
339A ILE* 2.7 47.8 + - + +
341A PHE* 4.0 19.5 - - + -
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Residues in contact with PRO 184 (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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182A TYR 4.4 0.2 - - - +
183A THR* 1.3 97.9 + - - +
185A ILE* 1.3 65.6 + - - +
186A ARG* 3.4 6.9 + - - +
192A GLU 3.7 5.4 - - - +
193A VAL* 4.0 9.4 - - - +
194A ILE* 4.9 1.4 + - - +
280A MET* 3.2 33.4 - - + +
281A GLY 3.4 21.5 - - - +
282A GLU* 4.8 4.7 - - + -
337A LYS 4.1 6.5 - - - +
338A ARG* 4.4 3.6 - - + -
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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