Contacts of the strand formed by residues 368 - 373 (chain A) in PDB entry 6R4E
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 ARG 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A CYS 3.7 1.2 - - - -
367A ARG* 1.3 80.7 - - + +
369A LEU* 1.3 80.8 + - - +
370A ILE* 3.7 14.0 - - + +
394A LEU* 4.4 1.9 - - - +
395A PRO* 3.6 26.9 - - + +
397A MET* 3.6 33.4 - - - +
409A THR* 5.7 0.2 - - - +
410A PRO* 3.2 22.6 + - - +
412A PHE* 3.8 13.9 - - - -
414A ASP 3.9 1.8 + - - -
415A ASP* 2.8 44.6 + - - +
416A VAL* 2.9 28.1 + - - +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ILE* 5.5 0.7 - - + -
368A ARG* 1.3 80.2 - - - +
370A ILE* 1.3 64.2 + - - +
371A LEU* 4.7 6.7 - - + -
388A LEU* 4.3 14.6 - - + -
392A THR* 4.3 15.3 - - + -
394A LEU* 3.3 33.7 - - + -
395A PRO 3.0 11.8 + - - +
396A VAL* 3.4 18.2 - - + -
397A MET 2.9 25.0 + - - -
416A VAL* 3.3 14.4 - - + +
418A PHE* 4.1 16.4 - - + -
488A PHE* 3.8 27.1 - - + -
492A MET* 5.0 5.6 - - + -
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ARG* 3.7 41.7 - - + +
369A LEU* 1.3 77.9 - - - +
371A LEU* 1.3 60.6 + - - +
372A ILE* 3.8 24.8 + - + +
397A MET* 3.2 19.7 - - + +
399A GLU* 4.3 14.6 - - + -
404A PHE* 4.6 3.8 - - + -
410A PRO 4.9 0.4 - - - +
411A VAL* 4.6 11.9 - - + -
415A ASP* 3.9 13.7 - - + +
416A VAL 2.8 10.4 + - - +
417A CYS* 3.3 21.4 - - - +
418A PHE* 2.7 33.8 + - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 4.7 7.2 - - + -
370A ILE* 1.3 78.9 - - - +
372A ILE* 1.3 59.9 + - - +
373A ALA* 5.5 0.4 - - - -
381A GLY* 3.8 28.5 - - - +
384A THR* 4.6 1.6 - - - +
388A LEU* 3.8 30.3 - - + -
396A VAL* 4.4 7.4 - - + -
397A MET 2.8 15.2 + - - +
398A VAL* 4.0 16.7 - - + +
399A GLU* 2.7 33.3 + - - +
418A PHE* 3.6 34.8 - - + -
420A LEU* 4.6 12.1 - - + -
485A LEU* 4.8 9.4 - - + -
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE* 3.8 17.7 - - + -
371A LEU* 1.3 78.5 - - - +
373A ALA* 1.3 67.4 + - - +
399A GLU* 3.4 12.6 - - + +
401A ALA* 3.9 28.0 - - + -
404A PHE* 3.6 40.4 - - + -
417A CYS* 4.7 3.8 - - + -
418A PHE 2.9 10.6 + - - +
419A PHE* 3.4 37.5 - - + -
420A LEU* 3.3 18.8 + - - +
429A THR* 3.9 5.8 - - - +
432A GLY* 4.9 4.5 - - - -
436A CYS* 3.9 7.4 - - - -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LEU 4.3 0.9 - - - -
372A ILE* 1.3 80.4 - - - +
374A CYS* 1.3 64.6 + - - +
377A SER* 3.6 6.3 - - - +
378A TYR* 3.5 28.7 - - - +
399A GLU 3.3 5.7 + - - +
400A LEU* 3.5 8.8 - - - -
401A ALA 2.9 20.6 + - - -
420A LEU* 3.4 30.3 - - + +
429A THR* 4.0 7.4 - - - -
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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