Contacts of the strand formed by residues 376 - 380 (chain B) in PDB entry 5H14
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 MET 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TYR* 3.5 44.2 - - + +
82B PHE* 3.8 19.7 - - - -
370B MET* 3.2 27.0 - - - +
371B ASP* 3.0 27.1 + - - +
375B LYS* 1.3 76.9 - - + +
377B LEU* 1.3 59.0 + - - +
388B VAL* 4.2 6.7 - - + -
389B TRP 3.4 7.6 - - - +
391B LEU* 4.0 3.6 - - - -
418B PHE* 3.6 32.7 - - + -
422B SER* 3.6 23.6 - - - +
439B ARG* 4.3 12.1 - - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.2 10.5 - - + -
328B ILE* 4.0 11.2 - - + -
356B PHE* 3.9 36.1 - - + -
368B PHE* 3.6 34.1 - - + -
369B SER 3.4 10.8 - - - +
370B MET* 3.8 11.0 - - + -
376B MET* 1.3 73.2 - - - +
378B ALA* 1.3 62.0 + - - +
388B VAL* 3.2 7.6 - - - +
389B TRP* 2.9 56.7 + - + +
391B LEU* 4.0 18.6 - - + +
418B PHE* 4.7 0.4 - - - -
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Residues in contact with ALA 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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368B PHE* 3.2 6.3 - - - +
369B SER 2.8 33.8 + - - +
377B LEU* 1.3 76.2 - - - +
379B LEU* 1.3 60.3 - - - +
386B LEU* 4.0 12.1 - - + -
387B TYR 3.2 9.9 - - - +
388B VAL* 4.3 3.8 - - + -
389B TRP* 4.5 2.2 - - - -
416B THR* 3.8 16.9 + - - +
418B PHE* 3.7 27.6 - - + -
425B LEU* 4.5 2.2 - - + -
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Residues in contact with LEU 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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322B LYS* 4.3 4.9 - - - -
328B ILE* 4.2 7.6 - - + -
358B TYR* 3.5 52.0 - - + +
361B CYS* 4.0 11.0 - - + -
366B MET 4.2 11.0 - - - +
367B ARG 3.4 30.1 - - - +
368B PHE* 4.0 9.2 - - + +
378B ALA* 1.3 77.0 - - - +
380B GLY* 1.3 73.2 + - - +
386B LEU* 4.2 3.4 - - - -
387B TYR* 2.8 44.9 + - + +
389B TRP* 4.1 10.7 - - + -
413B ILE 5.8 0.2 - - - +
416B THR* 5.1 1.1 - - - -
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Residues in contact with GLY 380 (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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361B CYS* 3.6 6.2 - - - -
366B MET* 3.7 5.4 - - - +
367B ARG 4.7 2.0 + - - -
379B LEU* 1.3 94.4 - - - +
381B ASN* 1.3 64.1 + - - -
385B LYS 3.3 9.2 - - - -
386B LEU* 4.3 2.9 - - - -
413B ILE* 3.7 30.3 + - - +
416B THR* 4.4 7.3 - - - +
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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