Contacts of the strand formed by residues 370 - 376 (chain D) in PDB entry 5Y7K
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 SER 370 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364D PHE* 3.3 6.8 - - - -
365D THR* 2.9 43.1 + - - +
367D ASP* 4.6 0.9 + - - -
368D GLY 3.4 1.0 - - - -
369D ASN* 1.3 80.1 + - - +
371D PHE* 1.3 61.3 + - - +
386D TYR* 3.0 27.4 + - - -
387D PHE 3.1 19.3 - - - -
388D GLN* 3.8 9.8 + - - -
389D ILE* 3.8 6.4 - - - +
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Residues in contact with PHE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D MET* 3.6 33.2 - - + -
327D ILE* 4.2 5.2 - - + -
345D HIS* 4.2 14.4 - + + -
362D PRO* 3.8 13.0 - - + -
363D HIS 3.2 19.1 - - - +
364D PHE* 3.4 31.4 - + + -
370D SER* 1.3 76.9 - - - +
372D TYR* 1.3 68.2 + - - +
373D LYS* 4.1 15.3 - - + -
386D TYR* 3.5 3.9 - - - -
387D PHE* 2.9 74.9 + + + +
388D GLN 4.8 0.9 - - - -
389D ILE* 3.6 15.0 - - + -
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Residues in contact with TYR 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D PRO* 3.7 0.7 - - - +
363D HIS* 2.9 44.2 + - + +
365D THR* 4.1 10.9 - - + +
371D PHE* 1.3 75.6 - - - +
373D LYS* 1.3 62.8 + - - +
384D ILE* 3.9 17.0 - - + -
385D CYS 3.4 4.0 - - - -
386D TYR* 3.6 53.2 + + + -
397D ILE* 4.1 15.7 - - + -
407D ILE* 3.8 9.6 - - + +
410D LEU* 3.9 27.6 - - + -
415D LEU* 3.5 26.9 - - + -
436D LEU* 3.4 29.0 - - + +
439D TYR* 4.3 5.3 + + - -
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Residues in contact with LYS 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D GLN* 2.5 35.6 + - - +
323D SER* 5.7 0.4 + - - -
325D MET* 4.7 10.0 - - - +
347D GLU* 3.1 29.8 + - - +
359D PRO* 4.2 0.2 - - - +
360D SER* 3.1 34.8 - - - +
361D GLU 4.3 7.0 - - - +
362D PRO* 4.6 7.2 - - + -
371D PHE* 4.1 23.6 - - + -
372D TYR* 1.3 76.4 - - - +
374D ILE* 1.3 70.5 + - - +
375D ILE* 3.6 7.5 + - + +
384D ILE* 4.4 2.0 - - - -
385D CYS* 2.8 34.6 + - - +
387D PHE* 4.1 10.3 - - + -
407D ILE* 4.3 4.0 - - - +
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Residues in contact with ILE 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D GLU* 4.2 2.9 - - - +
356D ARG* 4.6 6.7 - - - +
360D SER* 2.7 36.9 + - - +
361D GLU* 5.1 3.1 + - - +
373D LYS* 1.3 74.6 - - - +
375D ILE* 1.3 69.2 + - - +
382D ARG* 3.8 28.1 + - + -
383D HIS* 3.2 13.7 - - - +
384D ILE* 4.4 9.4 - - + -
404D VAL* 3.9 25.4 - - + +
405D ILE 4.1 3.1 - - - +
406D GLY* 3.7 30.1 - - - +
407D ILE* 4.1 20.6 - - + +
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Residues in contact with ILE 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D GLU* 3.4 36.3 - - + +
373D LYS* 4.1 14.6 - - + +
374D ILE* 1.3 80.2 - - - +
376D SER* 1.3 65.6 - - - +
377D ASN 3.5 1.0 + - - -
382D ARG* 4.2 8.1 - - - +
383D HIS 3.0 29.7 + - - +
385D CYS* 3.8 4.5 - - + -
387D PHE* 3.8 14.8 - - + -
394D CYS* 3.7 30.5 - - - -
396D PHE* 3.4 25.5 - - + -
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Residues in contact with SER 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D GLU* 5.1 1.0 + - - -
375D ILE* 1.3 78.8 - - - +
377D ASN* 1.3 63.4 + - - +
380D GLY* 3.5 16.3 + - - -
381D TYR 3.9 4.8 - - - -
382D ARG* 4.2 21.2 - - - +
396D PHE* 4.0 5.2 - - - -
588D ASP* 2.6 32.7 + - - -
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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