Contacts of the strand formed by residues 353 - 361 (chain B) in PDB entry 4Y2H
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 LEU 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TYR 3.9 12.6 - - - +
160B GLY* 4.1 15.3 - - - +
162B LEU* 4.1 10.3 - - + -
163B HIS* 3.2 28.2 + - + +
236B ILE* 3.8 13.6 - - + +
290B ILE* 4.9 2.0 - - + -
343B LEU* 4.0 21.8 - - + -
344B LEU 3.9 2.0 - - - +
346B SER* 4.0 2.0 + - - -
352B ARG* 1.3 71.6 - - - +
354B ARG* 1.3 72.7 + - - +
355B VAL* 4.1 8.1 - - + -
372B ALA* 3.6 2.3 - - - -
373B MET* 2.9 51.2 + - + -
403B GOL 3.5 23.6 + - - -
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Residues in contact with ARG 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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342B THR 3.7 0.3 - - - +
343B LEU* 3.4 4.5 - - - -
344B LEU* 2.7 63.1 + - + +
345B PRO 4.0 14.7 + - - +
346B SER* 3.9 18.2 - - - +
347B ARG* 5.2 13.4 - - - +
352B ARG 3.4 0.2 + - - -
353B LEU* 1.3 75.1 - - - +
355B VAL* 1.3 69.5 + - - +
356B LEU* 4.2 16.4 - - - +
370B ASP* 2.7 36.7 + - - +
371B PHE 3.4 12.8 - - - +
372B ALA* 5.2 1.8 - - + -
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 3.6 24.0 - - + +
290B ILE* 4.7 5.8 - - + -
323B LEU* 3.8 24.5 - - + -
341B ILE* 3.7 32.5 - - + -
342B THR 3.3 2.2 - - - +
343B LEU* 3.9 16.8 - - + -
353B LEU* 4.1 9.0 - - + -
354B ARG* 1.3 82.4 - - - +
356B LEU* 1.3 66.1 + - - +
357B LEU* 3.7 2.7 + - + +
369B LYS 3.8 0.5 - - - +
370B ASP* 3.5 3.1 - - - -
371B PHE* 2.8 42.8 + - + -
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Residues in contact with LEU 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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340B GLU 3.7 1.2 - - - +
341B ILE* 3.4 4.7 - - - -
342B THR* 2.9 45.6 + - - +
344B LEU* 4.7 9.7 - - + +
354B ARG* 4.2 20.1 - - - +
355B VAL* 1.3 73.1 - - - +
357B LEU* 1.3 61.2 + - - +
358B ARG* 4.2 4.3 - - - -
368B THR* 4.7 14.4 - - + -
369B LYS 4.0 2.7 - - - +
370B ASP* 3.9 24.0 - - + +
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Residues in contact with LEU 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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193B ILE* 4.4 10.8 - - + -
275B PHE* 4.3 13.7 - - + -
288B PHE* 3.6 31.6 - - + -
323B LEU* 4.5 7.6 - - + -
325B LEU* 5.1 2.5 - - + -
340B GLU 3.5 14.6 - - - +
341B ILE* 4.2 15.5 - - + -
355B VAL* 3.7 5.3 + - + -
356B LEU* 1.3 74.3 - - - +
358B ARG* 1.3 67.7 - - - +
359B TYR* 3.7 18.6 - - + -
367B LYS 3.8 0.7 - - - +
368B THR* 3.4 7.2 - - - +
369B LYS* 2.8 46.2 + - + +
371B PHE* 4.0 25.1 - - + -
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Residues in contact with ARG 358 (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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274B ARG* 5.7 2.7 - - - +
339B GLY* 3.1 3.8 - - - -
340B GLU* 2.7 62.5 + - + +
356B LEU* 4.1 4.4 + - - -
357B LEU* 1.3 76.1 - - - +
359B TYR* 1.3 62.9 + - - +
366B GLU* 2.4 52.5 + - - +
367B LYS 3.4 3.3 + - - +
368B THR* 3.4 26.1 + - - -
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Residues in contact with TYR 359 (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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275B PHE* 4.7 0.9 - - + -
288B PHE* 3.7 26.0 - + + -
325B LEU* 3.5 40.6 - - + +
326B ASN* 4.8 4.7 + - - -
327B GLU* 5.5 2.1 + - - -
338B SER 3.4 7.2 - - - +
339B GLY* 4.0 0.9 - - - -
357B LEU* 3.7 24.0 - - + -
358B ARG* 1.3 75.4 - - - +
360B LYS* 1.3 63.4 + - - +
361B VAL* 4.0 22.4 - - + -
364B GLN* 4.5 12.5 + - - -
365B GLU 4.3 0.7 - - - +
366B GLU* 3.5 4.2 - - - +
367B LYS* 2.8 80.2 + - + +
368B THR 4.6 1.6 - - - -
369B LYS* 4.8 14.2 - - + +
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Residues in contact with LYS 360 (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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336B ASP 3.6 1.7 - - - +
337B VAL* 3.3 6.1 - - - +
338B SER* 2.7 48.2 + - - +
359B TYR* 1.3 79.6 - - - +
361B VAL* 1.3 63.2 + - - +
362B GLY 3.3 16.7 + - - +
363B ASP* 4.2 5.7 + - - +
364B GLN 2.7 34.7 + - - +
365B GLU* 4.5 3.7 - - - +
366B GLU* 4.2 29.6 - - + +
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Residues in contact with VAL 361 (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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285B MET* 3.9 27.6 - - + -
325B LEU* 4.7 4.7 - - + -
329B VAL* 4.4 15.8 - - + +
331B VAL* 3.7 30.5 - - + -
335B THR* 4.1 5.8 - - + -
336B ASP 3.6 1.8 - - - -
337B VAL* 4.2 9.9 - - + -
359B TYR* 4.0 22.1 - - + -
360B LYS* 1.3 77.5 - - - +
362B GLY* 1.3 71.6 + - - +
364B GLN* 3.1 36.1 + - - +
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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