Contacts of the strand formed by residues 369 - 373 (chain B) in PDB entry 6NYY
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 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B LYS 3.8 0.3 - - - +
298B VAL* 3.6 1.7 - - - +
299B LEU* 3.0 59.4 + - + +
358B ALA* 3.8 14.6 - - + -
362B ALA* 3.5 27.6 - - + +
367B VAL 4.8 1.1 - - - +
368B PRO* 1.3 76.5 - - - +
370B ILE* 1.3 70.1 + - - +
371B THR* 3.6 18.2 - - + -
403B ILE* 3.6 41.1 - - + -
405B PHE* 3.6 23.3 - - + -
441C PHE* 3.5 37.7 - + - -
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA* 5.3 1.3 - - + -
297B LYS 3.9 4.9 - - - +
298B VAL* 3.7 35.7 - - + +
368B PRO* 5.8 0.4 - - + -
369B PHE* 1.3 83.4 - - - +
371B THR* 1.3 61.2 + - - +
392B LEU* 4.2 8.5 - - + +
395B LEU* 3.9 15.7 - - + -
396B ALA* 3.7 41.1 - - + +
399B ASN* 5.0 5.2 - - + +
402B CYS* 4.4 6.1 - - + -
403B ILE 3.3 13.6 + - - +
404B LEU* 3.3 23.5 - - + +
405B PHE 3.1 22.0 + - - -
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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
----------------------------------------------------------
295B THR 4.7 0.7 - - - +
296B ALA* 3.8 14.6 - - - -
297B LYS 3.9 7.9 + - - +
299B LEU* 3.8 21.3 - - + -
369B PHE* 3.6 14.6 - - + -
370B ILE* 1.3 75.0 - - - +
372B VAL* 1.3 80.7 + - - +
404B LEU* 5.0 1.3 - - - -
405B PHE* 3.4 12.7 + - - -
407B ASP* 5.4 0.2 - - - +
441C PHE* 3.5 40.9 - - + +
442C ASN* 4.7 6.5 - - - +
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR 4.3 7.6 - - - +
295B THR 5.3 0.2 - - - -
296B ALA* 3.7 21.5 - - + -
371B THR* 1.3 88.1 + - - +
373B SER* 1.3 72.8 + - - +
376B GLU* 3.6 18.8 - - - +
377B PHE* 3.8 11.7 - - + -
392B LEU* 3.8 26.0 - - + -
404B LEU* 5.3 0.7 - - + -
405B PHE 3.2 2.6 + - - +
406B ILE* 3.8 28.0 - - + -
407B ASP* 3.2 21.1 + - - +
436C VAL* 5.4 2.9 - - - +
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Residues in contact with SER 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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372B VAL* 1.3 89.3 - - - +
374B GLY* 1.3 61.9 + - - +
375B SER* 3.2 7.2 + - - -
376B GLU* 3.2 27.2 + - - +
377B PHE* 4.3 4.3 - - - -
406B ILE* 4.2 1.1 - - - -
407B ASP 3.3 12.3 - - - -
408B GLN* 5.4 0.9 - - - -
432C ASN 5.1 0.2 - - - -
433C GLN* 3.2 24.1 + - - -
436C VAL* 3.7 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