Contacts of the strand formed by residues 399 - 407 (chain B) in PDB entry 2YA6
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 VAL 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B ASP 4.9 1.1 - - - +
358B TRP* 4.2 18.8 - - + -
359B GLY 3.9 14.6 - - - +
361B ILE* 4.2 5.6 - - + -
384B LEU* 4.7 1.3 - - - -
397B SER 3.5 14.8 - - - +
398B PRO* 1.3 73.0 - - - +
400B ASN* 1.3 79.4 + - - +
401B ILE* 3.8 19.5 - - + -
420B MET* 3.2 6.9 - - - +
421B PHE* 2.9 50.4 + - + +
422B PRO 4.2 8.5 - - - +
424B GLY 4.0 17.0 - - - +
426B GLY* 4.5 3.8 - - - +
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Residues in contact with ASN 400 (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 ILE* 3.1 39.9 + - - +
363B MET* 3.8 23.1 - - + +
382B THR* 3.4 22.8 - - - +
384B LEU* 3.5 20.3 + - - +
398B PRO 4.1 2.0 + - - -
399B VAL* 1.3 73.6 + - - +
401B ILE* 1.3 63.4 - - - +
418B TYR* 3.6 20.5 - - + -
419B ASP 3.0 16.7 + - - +
420B MET* 3.5 22.6 - - - +
522B TRP* 3.7 3.2 - - - -
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Residues in contact with ILE 401 (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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349B ASP* 3.4 13.2 - - - +
351B ARG* 3.4 18.2 - - - +
357B ASP* 3.6 39.5 - - + +
361B ILE* 4.3 3.4 - - + -
363B MET* 3.9 4.9 - - - +
399B VAL* 3.8 11.2 - - + -
400B ASN* 1.3 76.2 - - - +
402B ASP* 1.3 87.5 + - - +
419B ASP* 3.0 42.2 + - + +
421B PHE* 3.8 20.6 - - + -
1777B DAN 3.8 15.7 - - + +
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Residues in contact with ASP 402 (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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333B ILE* 3.4 16.2 - - - +
349B ASP* 3.0 17.6 + - - -
363B MET* 4.3 0.8 - - - +
401B ILE* 1.3 85.0 - - - +
403B MET* 1.3 62.1 + - - +
418B TYR* 3.1 19.2 - - - -
419B ASP* 4.0 3.6 - - - +
550B PHE* 5.8 0.2 - - - -
553B VAL* 3.2 23.6 - - + +
555B PRO* 3.9 18.2 - - + +
575B TYR* 4.8 2.4 + - - -
632B GLU* 4.6 1.7 - - - +
1777B DAN 2.7 54.7 + - - +
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Residues in contact with MET 403 (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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333B ILE* 4.3 11.8 - - - +
335B ALA* 4.0 14.6 - - + +
347B GLY* 4.1 10.8 - - - -
348B ALA 3.7 33.0 - - - +
349B ASP* 4.4 2.2 + - - +
363B MET* 3.9 24.7 - - + -
364B VAL 3.9 8.3 - - - +
365B ILE* 4.7 0.2 - - - -
381B ILE* 4.3 6.7 - - + -
402B ASP* 1.3 75.2 - - - +
404B VAL* 1.3 65.9 + - - +
405B LEU* 3.9 21.5 - - - -
416B SER* 3.6 22.4 - - - +
417B ILE 3.2 8.3 - - - +
418B TYR* 4.0 6.3 - - + -
553B VAL* 4.2 0.2 - - - -
555B PRO* 3.3 5.0 - - - +
556B GLY* 3.0 21.8 + - - +
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Residues in contact with VAL 404 (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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403B MET* 1.3 77.6 - - - +
405B LEU* 1.3 65.3 + - - +
406B VAL* 5.6 0.3 - - - +
415B PHE 3.5 1.6 - - - +
416B SER* 3.4 4.7 - - - -
417B ILE* 2.8 36.7 + - + +
553B VAL* 3.5 24.5 - - + -
554B GLY 3.2 26.2 - - - +
555B PRO* 3.9 0.7 - - + -
556B GLY 3.0 7.2 - - - +
557B THR 4.0 1.1 - - - -
558B GLY* 3.4 30.1 - - - +
572B ILE* 4.1 29.1 - - + +
573B PRO* 4.3 5.4 - - + +
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Residues in contact with LEU 405 (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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335B ALA* 3.8 31.9 - - + +
337B LEU* 4.1 20.6 - - + -
345B ILE* 4.1 23.1 - - + +
347B GLY* 4.2 6.1 - - - +
365B ILE* 4.7 3.4 - - + -
403B MET* 3.9 15.3 - - - -
404B VAL* 1.3 71.8 - - - +
406B VAL* 1.3 56.8 + - - +
414B ILE* 4.5 6.1 - - + -
415B PHE 3.2 13.5 - - - +
416B SER* 3.9 19.3 - - - -
533B TRP* 4.1 16.2 - - + -
556B GLY 2.9 9.8 + - - +
557B THR* 3.3 9.8 - - - +
558B GLY 2.7 31.7 + - - -
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Residues in contact with VAL 406 (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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337B LEU* 3.9 12.0 - - + +
404B VAL 5.6 0.4 - - - +
405B LEU* 1.3 76.4 - - - +
407B GLN* 1.3 63.7 + - - +
414B ILE* 3.4 2.1 - - - +
415B PHE* 2.7 53.9 + - + +
558B GLY* 3.7 29.2 - - - +
559B ILE* 3.9 6.3 - - - +
560B VAL* 3.9 25.1 - - + -
570B ILE* 3.7 22.0 - - + -
572B ILE* 3.8 13.9 - - + -
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Residues in contact with GLN 407 (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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337B LEU* 3.9 15.7 - - + +
338B LYS 4.4 2.1 - - - +
339B THR* 3.4 11.6 - - - -
340B ASP* 2.9 49.9 + - - +
406B VAL* 1.3 77.6 - - - +
408B ASP* 1.3 75.9 + - - +
409B PRO* 3.4 6.5 - - + +
412B LYS* 2.8 26.2 + - - +
413B ARG 3.3 9.9 - - - +
414B ILE* 3.9 17.8 - - + +
529B ASP* 5.1 0.6 + - - +
560B VAL* 3.3 20.6 - - - +
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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