Contacts of the strand formed by residues 351 - 357 (chain B) in PDB entry 4ZSQ
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 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.5 43.8 + - + -
191B THR 3.2 15.0 - - - +
192B PRO* 4.3 0.4 - - + -
193B ILE* 3.7 6.8 - - - +
290B GLU* 2.7 51.3 + - - +
346B ASP* 2.8 58.2 + - + +
349B ARG* 3.2 52.2 - - - +
350B LYS* 1.3 78.0 - - - +
352B ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B TRP 3.6 1.2 - - - +
190B TYR* 3.1 4.0 - - - -
191B THR* 2.6 51.1 + - + +
193B ILE* 3.6 24.7 - - + +
199B TYR* 3.8 26.5 - - + +
201B VAL* 3.9 19.7 - - + -
227B VAL* 4.4 7.6 - - + -
343B VAL* 3.6 25.1 - - + -
344B VAL 3.3 11.0 - - - +
345B PHE* 4.3 11.0 - - + -
351B ARG* 1.3 80.1 - - - +
353B GLY* 1.3 62.1 + - - +
354B PHE* 3.7 17.2 - - + -
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Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.2 4.9 - - - -
189B TRP 3.3 4.0 - - - -
190B TYR* 3.3 28.0 - - - -
342B TYR 3.6 0.2 - - - +
343B VAL* 3.4 10.4 - - - +
344B VAL* 2.8 36.5 + - - -
352B ILE* 1.3 73.9 - - - +
354B PHE* 1.3 61.4 + - - -
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Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B SER 3.6 0.2 - - - +
188B LEU* 3.4 5.0 - - - +
189B TRP 2.8 33.6 + - - +
191B THR* 4.0 9.9 - - + -
201B VAL* 5.7 0.9 - - + -
227B VAL* 4.3 11.7 - - + -
287B LEU* 3.8 21.5 - - + -
296B PHE* 4.2 10.1 - + + -
298B ILE* 3.9 30.5 - - + -
333B MET* 3.5 33.0 - - + -
337B ILE* 5.8 0.4 - - + -
338B MET* 6.2 1.1 - - + -
341B PHE* 4.1 20.4 - + + -
342B TYR 3.6 2.7 - - - -
343B VAL* 4.1 18.2 - - + -
352B ILE* 3.7 30.1 - - + -
353B GLY* 1.3 76.3 - - - -
355B ALA* 1.3 59.5 - - - +
370B VAL* 3.6 11.8 - - + +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TYR* 3.4 41.1 - - + -
185B THR 4.1 0.9 - - - +
187B SER 3.7 12.3 - - - +
188B LEU* 3.7 12.1 - - + -
341B PHE* 3.1 6.4 - - - -
342B TYR* 2.7 37.2 + - + -
354B PHE* 1.3 74.3 - - - +
356B VAL* 1.3 58.9 - - - +
370B VAL* 3.9 9.0 - - - -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TYR* 3.4 4.9 - - - +
185B THR* 3.2 45.9 + - - +
186B GLY* 6.1 1.1 - - - -
187B SER 5.1 0.2 + - - -
340B GLY 4.0 4.7 - - - +
341B PHE* 4.2 3.1 - - + -
355B ALA* 1.3 72.5 - - - +
357B SER* 1.3 63.7 + - - +
360B HIS* 3.4 34.5 - - + +
367B THR* 5.9 0.2 - - - -
368B ALA 3.6 8.1 - - - +
369B ALA* 3.6 34.3 - - - +
370B VAL* 3.6 11.9 - - + +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLN* 3.4 24.6 - - - +
154B LEU 5.0 0.6 + - - -
183B LEU 3.9 3.6 - - - -
185B THR* 5.2 0.4 + - - -
339B GLU 4.3 3.8 - - - -
340B GLY 2.9 29.7 + - - -
341B PHE 3.7 11.4 + - - -
342B TYR 4.1 3.6 - - - +
355B ALA 3.3 1.6 + - - -
356B VAL* 1.3 74.2 - - - +
358B ALA* 1.3 61.9 + - - +
359B CYS* 3.0 15.5 + - - -
360B HIS* 2.7 36.3 + - - -
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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