Contacts of the strand formed by residues 338 - 344 (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 ARG 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TYR* 3.5 45.5 + - + -
178A THR 3.3 16.2 - - - +
179A PRO* 4.4 0.7 - - + -
180A ILE* 3.7 6.0 - - - +
277A GLU* 2.9 38.3 + - - +
333A ASP* 2.9 59.0 + - + +
336A ARG* 3.1 58.1 - - + +
337A LYS* 1.3 79.9 - - - +
339A ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 339 (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 TRP 3.7 1.0 - - - +
177A TYR* 3.3 3.7 - - - -
178A THR* 2.8 43.9 + - + +
180A ILE* 3.8 17.5 - - + -
186A TYR* 3.8 29.6 - - + -
188A VAL* 3.8 22.2 - - + -
214A VAL* 4.1 9.2 - - + -
330A VAL* 3.7 18.8 - - + -
331A VAL 3.1 12.1 - - - +
332A PHE* 4.3 12.1 - - + -
338A ARG* 1.3 78.4 - - - +
340A GLY* 1.3 63.1 + - - +
341A PHE* 3.6 22.6 - - + -
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Residues in contact with GLY 340 (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 LEU* 3.8 10.1 - - - -
176A TRP 3.2 8.7 - - - -
177A TYR* 3.4 22.7 - - - -
329A TYR 3.5 0.2 - - - +
330A VAL* 3.3 8.3 - - - +
331A VAL* 2.8 33.2 + - - -
339A ILE* 1.3 73.7 - - - +
341A PHE* 1.3 65.4 + - - -
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Residues in contact with PHE 341 (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 0.2 - - - +
175A LEU* 3.5 2.7 - - - +
176A TRP 2.7 34.0 + - - +
178A THR* 4.2 8.1 - - + -
188A VAL* 5.8 0.2 - - + -
214A VAL* 4.6 12.3 - - + -
274A LEU* 3.7 21.3 - - + -
283A PHE* 4.0 10.3 - + + -
285A ILE* 4.1 33.7 - - + -
320A MET* 3.9 28.9 - - + -
324A ILE* 5.7 1.3 - - + -
325A MET* 5.8 3.4 - - + -
328A PHE* 4.5 10.5 - + + -
329A TYR 3.5 1.6 - - - -
330A VAL* 4.1 26.7 - - + -
339A ILE* 3.6 29.8 - - + -
340A GLY* 1.3 77.0 - - - -
342A ALA* 1.3 60.6 + - - +
357A VAL* 3.6 12.6 - - + +
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Residues in contact with ALA 342 (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* 3.4 37.5 - - + -
172A THR 4.3 0.4 - - - +
174A SER 3.5 14.4 - - - +
175A LEU* 3.6 11.9 - - + -
328A PHE* 3.3 7.1 - - - +
329A TYR* 2.7 34.2 + - + +
341A PHE* 1.3 77.3 - - - +
343A VAL* 1.3 59.7 + - - +
357A VAL* 3.9 9.6 - - - -
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Residues in contact with VAL 343 (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* 3.1 4.6 - - - +
172A THR* 2.9 49.3 + - - +
173A GLY* 6.4 0.2 - - - -
174A SER 4.9 0.6 + - - -
327A GLY 4.2 2.9 - - - -
328A PHE* 4.4 4.3 - - + -
342A ALA* 1.3 72.3 - - - +
344A SER* 1.3 61.9 + - - +
347A HIS* 3.4 41.1 - - + +
355A ALA 4.2 3.1 - - - +
356A ALA* 3.9 12.3 - - + +
357A VAL* 3.8 29.3 - - + +
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Residues in contact with SER 344 (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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153A GLN* 3.8 11.9 + - - +
170A LEU 3.2 16.6 - - - -
171A TYR* 4.1 0.4 - - - +
172A THR* 5.2 2.4 + - - -
327A GLY 3.0 26.0 + - - -
328A PHE 3.7 2.7 - - - -
329A TYR 3.6 17.3 - - - -
342A ALA 3.4 0.8 + - - -
343A VAL* 1.3 75.9 - - - +
345A ALA* 1.3 61.7 + - - +
346A CYS* 3.2 20.8 + - - -
347A HIS* 2.9 27.9 + - - -
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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