Contacts of the strand formed by residues 372 - 379 (chain C) 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 SER 372 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR* 3.6 1.5 - - - +
366C LYS* 2.8 23.0 + - - +
367C SER* 3.1 23.4 + - - -
370C SER* 2.9 19.7 + - - -
371C ARG* 1.3 73.6 - - - +
373C GLY* 1.3 63.6 + - - +
399C ALA 4.3 0.2 - - - -
400C ILE* 3.4 23.7 + - - -
401C THR 5.7 0.2 - - - -
402C ASP 3.4 7.3 + - - -
403C TRP* 3.7 16.3 - - - -
404C SER* 3.8 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR* 3.3 8.3 - - - -
366C LYS* 3.6 7.9 - - - -
372C SER* 1.3 74.4 - - - +
374C PHE* 1.3 63.7 + - - +
398C VAL* 2.8 22.4 - - - +
399C ALA 3.1 15.5 + - - -
402C ASP 2.8 13.9 + - - -
404C SER* 3.0 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C PHE* 3.9 2.9 - + - -
363C GLY* 3.8 9.9 - - - -
364C ARG* 3.1 42.2 - - - -
365C THR* 4.1 4.9 - - + +
366C LYS* 3.6 6.5 + - - +
373C GLY* 1.3 76.6 - - - +
375C GLU* 1.3 81.0 + - - +
376C MET* 4.2 2.0 - - - -
397C ILE* 3.0 28.2 + - + -
398C VAL* 2.6 44.0 + - + +
404C SER* 4.7 4.9 - - - -
405C GLY 5.0 4.0 - - - -
407C SER* 3.5 37.7 - - - -
422C PHE* 3.7 23.8 - + - -
424C VAL* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ARG* 5.2 0.2 + - - -
362C ILE 3.6 1.4 - - - +
363C GLY* 3.5 5.0 - - - -
364C ARG* 3.0 66.1 + - + +
365C THR 4.3 2.5 - - - +
366C LYS* 3.1 31.4 + - + +
374C PHE* 1.3 81.9 - - - +
376C MET* 1.3 66.0 + - - +
377C ILE* 3.2 6.8 - - + +
394C LYS* 2.8 44.1 + - + -
395C GLN 3.3 12.3 - - - +
396C ASP* 4.4 2.2 - - - +
397C ILE 4.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TRP* 3.6 54.7 - - + +
352C PHE* 4.0 21.8 - - + -
361C TRP* 3.8 22.2 - - + -
362C ILE 3.5 9.0 - - - +
363C GLY* 3.7 16.8 - - - -
374C PHE* 4.2 1.8 - - - -
375C GLU* 1.3 74.4 - - - +
377C ILE* 1.3 62.0 + - - +
392C VAL 3.9 0.3 - - - +
394C LYS* 3.3 4.9 - - - +
395C GLN* 2.7 44.8 + - + +
397C ILE* 4.0 8.5 - - + -
422C PHE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL* 3.7 18.4 - - + -
360C VAL 3.4 1.9 - - - +
361C TRP* 3.4 6.9 - - - -
362C ILE* 2.7 49.9 + - + +
364C ARG* 3.6 20.4 - - + +
375C GLU* 3.2 30.1 - - + +
376C MET* 1.3 80.5 - - - +
378C TRP* 1.3 64.7 + - - +
379C ASP* 3.7 3.5 + - + +
390C PHE* 3.6 39.0 - - + -
392C VAL 3.4 4.3 - - - +
394C LYS* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C TYR* 3.9 28.0 - + + -
359C GLY* 3.8 13.0 - - - -
360C VAL* 3.2 43.1 - - - -
361C TRP* 3.5 50.1 - + + -
377C ILE* 1.3 72.3 - - - +
379C ASP* 1.3 58.8 + - - +
380C PRO* 3.4 26.2 - - + +
390C PHE* 3.4 2.1 - - - +
391C SER* 2.9 45.0 + - - -
392C VAL* 3.0 23.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C SER* 2.9 27.8 + - - +
321C VAL* 3.9 4.6 - - + +
360C VAL* 3.2 31.5 + - + +
362C ILE* 4.8 6.7 - - + -
377C ILE* 3.7 2.3 + - + -
378C TRP* 1.3 73.4 - - - +
380C PRO* 1.3 92.0 - - - +
381C ASN 4.0 0.7 - - - +
382C GLY* 3.0 21.7 + - - -
387C ASP* 3.6 11.1 - - - +
389C SER 3.2 24.7 - - - +
390C PHE* 3.9 9.9 - - + -
----------------------------------------------------------
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