Contacts of the strand formed by residues 370 - 378 (chain B) in PDB entry 4RE1
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 PHE 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311B VAL* 3.6 22.7 - - + -
312B CYS 3.4 11.2 - - - -
346B TYR* 4.4 4.9 - + - -
347B MET* 3.5 30.5 - - + -
350B PHE* 3.5 42.2 - + + -
366B VAL 4.6 0.9 - - - +
367B LEU* 3.1 26.3 + - + +
368B GLU 3.5 0.8 - - - -
369B ASN* 1.3 78.9 - - - +
371B THR* 1.3 67.5 - - - +
372B ILE* 3.8 14.1 - - + -
391B VAL* 4.7 0.9 - - - +
392B PHE* 3.7 43.5 + + - -
68C LEU* 4.2 16.8 - - + -
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Residues in contact with THR 371 (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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250B LYS* 2.8 49.4 + - + +
251B PHE* 3.2 17.6 - - + -
311B VAL* 4.4 1.0 - - - +
312B CYS* 2.7 44.4 + - - +
315B GLY 5.4 0.2 + - - -
368B GLU 5.3 0.7 - - - +
369B ASN 4.2 1.1 - - - -
370B PHE* 1.3 84.6 - - - +
372B ILE* 1.3 65.3 + - - +
390B CYS 3.4 5.8 - - - -
391B VAL* 3.7 23.3 - - + -
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Residues in contact with ILE 372 (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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251B PHE* 3.6 4.9 - - - -
309B THR* 3.9 23.3 - - + -
310B LYS 3.3 11.0 - - - +
311B VAL* 4.2 14.8 - - + -
347B MET* 4.5 10.5 - - + -
370B PHE* 3.8 26.2 - - + -
371B THR* 1.3 80.5 - - - +
373B LEU* 1.3 65.7 + - - +
374B LEU* 4.7 4.7 - - + +
388B MET 3.7 0.9 - - - +
389B ALA 3.6 0.2 - - - -
390B CYS* 2.7 57.9 + - + +
392B PHE* 3.9 17.3 - - + -
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Residues in contact with LEU 373 (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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251B PHE* 3.8 21.0 - - + -
252B PRO* 5.7 3.1 - - + -
256B GLY 5.7 0.2 - - - +
257B GLY* 5.3 2.5 - - - -
258B LEU* 4.0 33.2 - - + +
261B LEU* 5.3 2.5 - - + -
308B SER 3.4 2.8 - - - +
309B THR* 3.6 1.0 - - - -
310B LYS* 2.8 64.1 + - + +
312B CYS* 5.0 2.0 - - - -
372B ILE* 1.3 74.6 - - - +
374B LEU* 1.3 59.5 + - - +
375B VAL* 3.9 21.2 + - + +
387B CYS* 3.7 23.8 - - - -
388B MET 3.6 10.1 - - - +
389B ALA* 3.9 17.0 - - + -
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Residues in contact with LEU 374 (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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206B PHE* 4.0 28.5 - - + -
297B TYR* 3.4 26.2 - - - +
307B CYS* 5.0 7.2 - - + -
308B SER 3.3 7.6 - - - +
309B THR* 4.3 15.3 - - + +
372B ILE* 5.1 4.3 - - + -
373B LEU* 1.3 74.2 - - - +
375B VAL* 1.3 67.7 + - - +
376B VAL* 3.5 18.4 - - + -
386B LEU 5.5 0.2 - - - +
387B CYS* 3.2 4.9 - - - -
388B MET* 2.8 67.6 + - + +
390B CYS* 5.1 7.0 - - - -
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Residues in contact with VAL 375 (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* 3.7 29.6 - - + -
306B THR 3.4 2.9 - - - +
307B CYS* 3.7 0.2 - - - -
308B SER* 2.9 45.9 + - - +
310B LYS* 5.5 7.4 - - + +
373B LEU* 3.9 28.5 - - + -
374B LEU* 1.3 79.2 - - - +
376B VAL* 1.3 62.6 + - - +
377B THR* 3.8 17.1 + - - +
384B THR* 4.4 11.2 - - + +
386B LEU 3.7 5.8 - - - +
387B CYS* 4.3 5.8 - - + -
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Residues in contact with VAL 376 (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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201B LEU* 3.5 25.8 - - + -
297B TYR* 3.7 24.5 - - + +
305B VAL* 4.4 9.9 - - + -
306B THR 3.3 7.6 - - - +
307B CYS* 4.0 15.0 - - - -
374B LEU* 3.5 26.2 - - + -
375B VAL* 1.3 73.3 - - - +
377B THR* 1.3 61.2 + - - +
384B THR* 3.7 2.6 - - - +
385B LEU* 2.7 36.1 + - + -
386B LEU* 2.7 28.6 + - + +
388B MET* 6.5 0.2 - - - -
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Residues in contact with THR 377 (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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305B VAL* 3.2 6.9 - - - +
306B THR* 2.9 47.6 + - - -
375B VAL* 3.8 17.7 + - - +
376B VAL* 1.3 77.1 + - - +
378B ASN* 1.3 77.0 + - - +
379B ARG* 3.2 0.8 + - - +
382B GLN* 3.7 29.8 - - - +
383B GLU 3.2 14.7 + - - +
384B THR* 4.6 3.7 + - - -
385B LEU* 3.8 5.6 - - - +
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Residues in contact with ASN 378 (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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303B MET* 3.8 28.5 - - - +
304B THR 3.6 10.4 + - - +
377B THR* 1.3 68.1 - - - +
379B ARG* 1.3 56.9 + - - +
380B ASP* 3.1 21.3 + - - +
381B THR* 3.1 33.9 + - - +
382B GLN* 2.7 36.4 + - - -
383B GLU* 2.9 18.7 + - + +
385B LEU* 3.5 21.1 - - + +
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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