Contacts of the strand formed by residues 373 - 379 (chain B) in PDB entry 5EWL
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 TRP 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B VAL* 5.5 0.2 - - + -
263B ALA* 4.2 20.1 + - + -
266B THR* 3.2 54.7 + - + +
268B THR 5.1 0.8 + - - -
269B VAL* 3.5 23.2 - - + +
273B PHE* 4.2 13.1 - + - -
277B LEU* 3.3 53.6 - - + -
279B SER* 4.0 12.8 - - - -
285B TRP* 5.3 7.8 + - + -
365B ILE* 3.5 38.8 - - + -
366B LEU 3.5 6.1 - - - -
367B LEU* 3.4 29.4 - - + -
368B ASN* 5.1 0.2 - - - -
372B LYS* 1.3 75.0 - - - +
374B GLU* 1.3 59.4 + - - +
375B ARG 4.5 0.2 + - - -
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Residues in contact with GLU 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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285B TRP* 5.7 0.2 - - - -
365B ILE* 3.1 8.2 - - - -
366B LEU* 2.8 44.1 + - + +
368B ASN* 3.5 31.0 + - + +
372B LYS 3.6 0.2 + - - -
373B TRP* 1.3 74.3 - - - +
375B ARG* 1.3 70.0 + - - +
376B VAL* 4.0 13.4 - - + +
387B LYS* 3.5 11.4 + - - +
388B TYR* 3.0 25.5 + - - -
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Residues in contact with ARG 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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283B ASP* 3.6 11.1 + - - -
285B TRP* 3.4 52.2 - - + +
286B ASP* 3.0 30.1 + - - -
363B VAL* 3.7 20.5 - - + +
364B ILE 3.6 6.1 - - - +
365B ILE* 4.2 1.1 - - - -
373B TRP 4.5 0.2 + - - -
374B GLU* 1.3 77.9 - - - +
376B VAL* 1.3 63.5 + - - +
377B GLY 3.8 0.2 - - - -
378B LYS* 3.4 44.8 - - - +
387B LYS* 4.1 11.8 + - - +
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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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164B TYR* 5.0 0.2 + - - -
364B ILE* 2.8 37.2 + - + +
365B ILE 3.8 1.1 - - - -
366B LEU* 3.6 34.8 - - + +
374B GLU* 4.0 11.4 - - + +
375B ARG* 1.3 78.1 - - - +
377B GLY* 1.3 53.6 + - - +
378B LYS* 5.4 0.4 - - - -
386B MET* 3.6 10.2 - - - +
387B LYS* 2.8 37.6 + - - +
388B TYR* 3.7 27.2 + - + -
391B TRP* 3.8 21.5 - - + -
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Residues in contact with GLY 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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363B VAL* 3.7 1.6 - - - +
364B ILE* 2.9 31.7 + - - +
375B ARG 3.8 1.0 - - - -
376B VAL* 1.3 80.6 - - - +
378B LYS* 1.3 79.7 + - - +
385B GLN 3.2 13.5 - - - -
386B MET* 3.9 11.7 - - - -
387B LYS 4.3 0.7 - - - -
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Residues in contact with LYS 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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283B ASP* 6.1 0.2 - - - +
362B LEU 3.6 11.2 - - - +
363B VAL* 4.6 3.6 - - + -
364B ILE* 3.8 5.9 - - - +
375B ARG* 3.4 57.2 - - - +
376B VAL 5.4 0.4 - - - -
377B GLY* 1.3 89.5 + - - +
379B TRP* 1.3 60.3 + - - +
380B LYS* 4.0 12.0 - - + -
383B SER 3.9 1.2 - - - +
384B LEU* 3.6 3.8 - - - +
385B GLN* 2.9 39.5 + - + +
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Residues in contact with TRP 379 (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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152B GLN* 5.3 9.3 - - + +
155B SER* 4.0 15.5 - - - -
156B VAL* 3.5 26.2 - - + +
159B ASN* 3.3 40.6 - - + -
360B PRO* 4.0 12.0 + - + +
361B LYS* 3.3 3.2 - - - -
362B LEU* 2.9 54.6 + - + +
364B ILE* 4.0 11.4 - - + +
378B LYS* 1.3 71.3 - - - +
380B LYS* 1.3 59.8 + - - +
382B LYS* 3.2 43.5 - - - +
383B SER 3.6 20.9 - - - -
384B LEU* 4.0 13.5 - - + -
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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