Contacts of the strand formed by residues 392 - 403 (chain G) in PDB entry 2HU4
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 392 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ASN 5.2 6.1 - - - +
361G TRP* 4.6 13.5 - - + -
376G MET 4.4 0.4 - - - -
377G ILE* 3.4 7.6 - - - +
378G TRP* 2.8 44.1 + - + -
390G PHE* 3.9 3.1 - - - -
391G SER* 1.3 92.3 - - - +
394G LYS* 1.3 74.8 + - - +
395G GLN* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 394 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ARG* 4.7 4.2 - - - +
366G LYS* 4.1 9.4 - - - +
375G GLU* 2.8 39.8 + - + +
376G MET 3.3 4.9 - - - +
377G ILE* 4.3 15.4 - - + +
390G PHE* 4.0 26.2 - - + -
392G VAL* 1.3 83.8 - - - +
395G GLN* 1.3 64.0 + - - +
396G ASP* 4.3 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 395 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G GLY* 3.7 6.7 - - - -
97G TRP* 2.9 67.7 + - + +
361G TRP* 4.9 4.3 - - + -
375G GLU* 3.3 2.0 - - - -
376G MET* 2.8 43.0 + - + +
392G VAL* 5.3 3.4 - - + -
394G LYS* 1.3 75.5 - - - +
396G ASP* 1.3 66.5 + - - +
397G ILE* 3.2 13.7 - - + +
446G PHE* 5.6 1.4 - - - -
453G THR* 3.6 9.7 + - - -
454G VAL* 3.5 13.4 - - - +
455G GLY* 4.0 16.8 - - - +
458G TRP* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G LYS* 2.8 29.9 + - - +
374G PHE 4.2 3.8 - - - +
375G GLU* 4.5 0.4 - - - +
394G LYS* 4.3 14.2 - - - +
395G GLN* 1.3 74.2 - - - +
397G ILE* 1.3 64.3 + - - +
398G VAL 5.0 2.0 - - - +
399G ALA* 6.5 0.2 - - - -
454G VAL 4.6 0.2 - - - +
455G GLY* 3.1 12.8 - - - -
456G TRP 3.0 39.5 + - - +
458G TRP* 4.2 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G TRP* 5.3 1.3 - - + -
374G PHE* 3.1 29.7 + - + +
376G MET* 3.9 17.5 - - + +
395G GLN* 3.2 29.6 - - + +
396G ASP* 1.3 83.4 - - - +
398G VAL* 1.3 81.8 + - + +
422G PHE* 3.9 20.6 - - + -
424G VAL* 4.5 1.6 - - + -
444G ILE* 3.9 7.4 - - + -
446G PHE* 3.9 31.2 - - + -
456G TRP 3.3 7.2 - - - +
458G TRP* 3.2 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G LYS* 3.2 7.0 - - - +
373G GLY* 4.0 2.2 - - - -
374G PHE* 2.9 41.3 + - + +
396G ASP* 5.6 2.0 - - - -
397G ILE* 1.3 99.7 - - + +
399G ALA* 1.3 73.0 + - - +
402G ASP* 3.8 26.5 - - + +
403G TRP 4.3 7.9 - - - +
404G SER* 5.1 1.3 - - - -
424G VAL* 5.4 0.2 - - + -
426G LEU* 4.6 7.4 - - + -
444G ILE* 3.9 16.8 - - + -
456G TRP 3.7 1.5 + - - -
457G SER* 4.0 10.1 - - - +
458G TRP 4.0 7.6 - - - +
459G PRO* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G LYS* 4.2 6.5 - - - +
373G GLY* 3.0 16.0 - - - -
396G ASP* 6.5 0.2 - - - -
398G VAL* 1.3 74.1 - - - +
400G ILE* 1.3 62.8 + - - +
401G THR* 3.1 21.1 - - + +
402G ASP* 3.1 15.6 + - - +
457G SER* 3.2 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G LYS* 3.5 43.7 - - + +
367G SER* 4.0 22.0 - - - +
372G SER* 3.4 18.4 + - - +
373G GLY* 4.1 7.4 - - - -
399G ALA* 1.3 68.8 - - - +
401G THR* 1.3 61.1 + - + +
402G ASP 3.1 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 401 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399G ALA* 3.8 10.6 - - + +
400G ILE* 1.3 81.6 - - + +
402G ASP* 1.3 73.0 + - - +
403G TRP* 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G SER* 4.5 2.9 - - - -
373G GLY* 2.7 32.9 + - - -
398G VAL* 3.8 13.7 - - + +
399G ALA* 3.1 4.8 + - - +
400G ILE 3.1 1.8 - - - -
401G THR* 1.3 94.9 + - - +
403G TRP* 1.3 61.0 + - - +
457G SER* 4.1 7.4 + - - -
459G PRO* 3.4 38.9 - - + +
461G GLY 5.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 403 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370G SER* 4.2 12.6 - - - -
371G ARG* 3.6 16.2 - - + +
372G SER* 3.4 26.9 - - - -
398G VAL* 4.3 5.0 - - - +
401G THR 5.8 0.4 - - - -
402G ASP* 1.3 79.4 + - - +
404G SER* 1.3 60.4 - - - +
426G LEU* 4.0 16.7 - - - +
427G ILE* 3.4 21.8 - - + +
428G ARG* 3.7 18.6 - - - -
432G LYS* 3.5 48.9 - - + -
433G GLU* 3.4 36.8 + - + +
460G ASP* 5.1 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G THR* 3.7 9.0 - - - +
371G ARG* 2.9 27.2 + - - +
372G SER 3.6 0.5 + - - -
373G GLY* 2.8 34.8 + - - -
374G PHE* 4.6 9.6 - - - -
398G VAL* 5.1 2.2 - - - -
402G ASP 3.5 0.4 + - - -
403G TRP* 1.3 73.3 - - - +
405G GLY* 1.3 66.2 + - - -
424G VAL* 4.6 7.4 - - - -
425G GLU 3.0 9.4 - - - -
426G LEU* 4.1 7.4 - - - -
427G ILE* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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