Contacts of the strand formed by residues 341 - 350 (chain B) in PDB entry 4YCV
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 GLU 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A PRO* 4.2 5.2 - - - +
277A MET* 2.6 44.7 + - - +
278A MET* 3.8 29.9 + - + +
327B LYS* 3.2 35.5 + - + +
328B VAL 3.6 3.8 - - - -
329B PHE* 3.9 15.7 - - + -
339B ASN* 3.1 22.4 + - - +
340B PRO* 1.3 77.7 - - - +
342B PHE* 1.3 60.8 + - - +
574B ILE* 4.4 4.9 - - - +
578B THR* 4.3 12.7 - - + +
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Residues in contact with PHE 342 (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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327B LYS* 4.4 4.5 - - - +
328B VAL* 2.9 60.7 + - + -
330B ARG* 3.3 50.5 - - + -
339B ASN 3.4 20.9 - - - +
340B PRO 4.3 1.3 - - - -
341B GLU* 1.3 75.2 - - - +
343B THR* 1.3 70.7 + - - +
344B SER* 3.5 11.8 + - - -
556B GLY* 5.3 8.5 - - - -
558B ASP* 3.3 18.4 - - - +
570B ILE* 4.9 8.3 - - + -
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Residues in contact with THR 343 (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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274A GLU* 2.7 44.1 + - - +
254B ARG* 3.4 14.6 + - - -
258B ILE* 5.0 1.1 - - + -
325B ILE* 4.2 21.3 - - + -
326B GLY 3.5 16.6 - - - +
327B LYS* 4.0 10.9 + - - +
342B PHE* 1.3 73.1 - - - +
344B SER* 1.3 62.4 + - - +
557B ILE* 3.2 27.5 + - + +
558B ASP* 3.0 18.6 + - - +
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Residues in contact with SER 344 (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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307B THR* 4.6 3.1 - - - +
324B GLU 3.7 1.4 - - - +
325B ILE* 3.5 1.4 - - - -
326B GLY 2.9 32.0 + - - +
328B VAL* 3.1 25.7 - - - +
342B PHE* 3.5 16.0 + - - -
343B THR* 1.3 76.3 - - - +
345B CYS* 1.3 61.6 + - - +
346B GLU* 3.9 20.9 + - - +
555B LEU 3.1 14.4 - - - -
557B ILE* 4.3 3.6 - - - -
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Residues in contact with CYS 345 (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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261B LEU* 3.6 30.3 - - + -
265B LEU* 4.0 21.3 - - - -
323B TYR* 4.6 0.7 - - - -
324B GLU 3.3 5.6 - - - -
325B ILE* 3.6 26.7 - - + -
344B SER* 1.3 75.3 - - - +
346B GLU* 1.3 68.0 + - - +
347B PHE* 4.3 3.1 + - - -
553B LEU* 4.0 1.6 - - - +
554B GLY* 3.2 2.4 - - - -
555B LEU* 2.9 42.8 + - + +
557B ILE* 4.1 8.2 - - + +
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Residues in contact with GLU 346 (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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306B ALA* 3.7 12.7 - - - +
307B THR* 3.1 39.3 + - - +
308B GLU* 3.3 25.2 + - - +
311B LEU* 3.5 8.8 - - + +
323B TYR* 3.2 3.1 - - - -
324B GLU 2.9 32.9 + - - -
328B VAL* 5.2 0.9 - - - +
330B ARG* 5.7 1.6 + - - -
344B SER* 3.9 18.0 + - - +
345B CYS* 1.3 78.4 - - - +
347B PHE* 1.3 61.9 + - - +
348B TYR* 4.3 6.7 + - + -
553B LEU 3.1 8.0 - - - +
554B GLY* 3.8 13.7 - - - -
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Residues in contact with PHE 347 (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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265B LEU* 4.4 7.9 - - + -
270B PHE* 3.4 30.5 - + + -
322B VAL 3.2 13.5 - - - +
323B TYR* 3.4 13.2 - - + -
345B CYS* 5.5 3.8 - - - -
346B GLU* 1.3 74.1 - - - +
348B TYR* 1.3 71.9 + - - +
349B TRP* 4.1 10.1 - + + -
357B LEU* 4.0 21.3 - - + -
360B TRP* 3.7 44.2 - + - -
551B GLY 4.9 0.4 - - - -
552B GLY* 3.2 3.5 - - - -
553B LEU* 2.9 75.6 + - + -
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Residues in contact with TYR 348 (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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270B PHE* 4.1 1.2 - - - -
308B GLU* 3.3 40.2 + - + +
311B LEU* 3.7 24.2 - - + -
312B LYS* 3.5 37.1 + - + -
315B ILE* 3.4 27.9 - - + +
320B ASP 3.5 0.9 - - - +
321B LYS* 3.5 1.0 - - - -
322B VAL* 2.9 36.5 + - + +
346B GLU* 4.3 9.4 + - + -
347B PHE* 1.3 80.6 - - - +
349B TRP* 1.3 61.0 + - - +
505B TYR* 3.7 11.0 + + - -
507B GLU* 4.0 9.6 - - + -
550B THR* 4.1 9.0 - - + -
551B GLY 3.5 6.7 - - - -
552B GLY* 3.6 24.4 - - - -
553B LEU 4.9 1.3 - - - -
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Residues in contact with TRP 349 (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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268B ARG* 6.3 2.2 - - - -
270B PHE* 4.2 11.9 - + + -
320B ASP 3.7 1.3 - - - -
321B LYS* 3.8 39.0 - - + +
347B PHE* 4.1 19.7 - + + -
348B TYR* 1.3 73.5 - - - +
350B ALA* 1.3 79.8 + - - +
351B TYR 5.2 1.0 + - - -
352B ALA* 3.5 23.4 - - + +
356B ASP* 3.9 35.9 - - + -
357B LEU* 4.1 12.1 - - + -
360B TRP* 4.3 18.2 - + + -
550B THR* 3.3 4.2 - - - +
551B GLY 2.9 36.5 + - - +
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Residues in contact with ALA 350 (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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108A ARG* 5.3 1.7 + - - -
315B ILE* 4.3 4.5 - - + -
320B ASP* 2.9 41.5 + - + +
349B TRP* 1.3 85.9 + - - +
351B TYR* 1.3 90.0 - - + +
352B ALA 3.2 0.9 + - - -
548B PRO* 4.1 15.3 - - + -
549B PRO 3.6 4.3 - - - -
550B THR* 3.7 4.8 - - - +
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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