Contacts of the strand formed by residues 171 - 179 (chain A) in PDB entry 4D88
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 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.8 16.8 - - + +
167A ASP 3.9 0.2 - - - -
168A HIS* 3.1 60.3 + - + +
169A SER 3.4 2.9 + - - -
170A LEU* 1.3 79.9 - - - +
172A THR* 1.3 72.6 + - - +
173A GLY 3.5 17.5 - - - -
175A LEU* 4.0 24.5 - - + +
329A TYR* 3.4 32.5 - + + -
342A ALA* 3.4 23.3 - - + -
343A VAL 3.1 14.4 - - - +
344A SER* 4.1 1.8 - - - +
345A ALA 4.8 0.2 - - - +
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Residues in contact with THR 172 (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 TYR* 1.3 82.7 - - - +
173A GLY* 1.3 68.7 + - - +
174A SER 3.9 0.2 + - - -
342A ALA* 4.3 0.5 - - - +
343A VAL* 2.9 41.5 + - - +
344A SER* 4.9 3.5 + - - +
345A ALA* 6.1 2.7 - - - +
347A HIS* 5.6 1.9 + - - -
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Residues in contact with GLY 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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171A TYR* 3.5 14.2 - - - -
172A THR* 1.3 80.8 - - - +
174A SER* 1.3 61.4 + - - -
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR 4.4 0.9 - - - +
173A GLY* 1.3 73.3 - - - -
175A LEU* 1.3 62.7 + - - +
176A TRP* 3.7 32.8 + - - -
341A PHE 3.7 3.5 - - - +
342A ALA* 3.5 16.7 - - - +
343A VAL 4.9 0.2 + - - -
357A VAL* 4.7 6.5 + - - +
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Residues in contact with LEU 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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166A ILE* 3.7 19.7 - - + -
171A TYR* 4.0 26.8 - - + +
173A GLY 3.9 1.2 + - - -
174A SER* 1.3 73.9 - - - +
176A TRP* 1.3 62.3 + - - +
177A TYR* 3.2 42.8 - - + +
329A TYR* 4.4 4.3 - - + +
331A VAL* 4.0 15.7 - - + -
340A GLY 3.8 6.1 - - - -
341A PHE 3.5 31.4 - - - +
342A ALA* 3.6 11.0 - - + +
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Residues in contact with TRP 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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174A SER* 3.7 29.4 - - - -
175A LEU* 1.3 74.8 - - - +
177A TYR* 1.3 62.9 + - - +
281A GLN* 5.6 2.7 - - + -
282A SER 5.0 2.0 - - - -
283A PHE* 3.5 48.1 - + + -
340A GLY* 3.2 1.2 - - - -
341A PHE 2.7 35.2 + - - -
357A VAL* 3.6 28.1 + - + -
358A GLU* 4.3 0.8 - - - +
359A GLY 3.2 31.1 - - - +
360A PRO* 3.4 37.2 - - + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.5 15.8 - - - +
175A LEU* 3.2 41.8 - - + +
176A TRP* 1.3 79.4 - - - +
178A THR* 1.3 60.0 + - - +
275A MET 3.9 0.7 - - - +
276A GLY* 3.9 1.0 - - - -
277A GLU* 3.6 38.7 + - + +
283A PHE* 3.4 10.5 - - - -
331A VAL* 4.6 4.5 - - + -
333A ASP* 4.4 10.6 + - + -
338A ARG* 3.5 60.6 + - + -
339A ILE 3.3 1.1 - - - -
340A GLY* 3.4 26.7 - - - -
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Residues in contact with THR 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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177A TYR* 1.3 74.1 - - - +
179A PRO* 1.3 67.9 + - - +
188A VAL* 3.9 28.7 - - + +
189A ILE 4.4 3.5 + - - -
274A LEU* 3.7 8.1 - - + +
275A MET* 2.7 29.5 + - - +
277A GLU* 5.1 0.4 - - - -
283A PHE* 3.8 11.4 - - - -
338A ARG* 3.3 3.8 - - - -
339A ILE* 2.8 46.3 + - + +
341A PHE* 4.2 13.5 - - + -
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Residues in contact with PRO 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 TYR 4.3 0.4 - - - +
178A THR* 1.3 92.3 + - - +
180A ILE* 1.3 66.4 + - - +
181A ARG* 3.4 5.1 + - - +
187A GLU 3.9 4.7 - - - +
188A VAL* 4.1 9.9 - - - +
189A ILE* 4.8 2.1 + - - +
275A MET* 3.3 33.3 - - + +
276A GLY 3.5 20.9 - - - +
277A GLU* 4.4 12.1 - - + +
337A LYS 3.8 8.3 - - - +
338A ARG* 4.3 2.7 - - + -
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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