Contacts of the strand formed by residues 356 - 361 (chain A) in PDB entry 1HMU
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 TYR 356 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 3.6 6.7 - - - +
351A HIS* 3.4 33.1 + + - -
353A ARG* 2.8 56.5 + - + +
354A PRO 3.4 0.8 + - - -
355A ALA* 1.3 88.5 - - + +
357A SER* 1.3 73.1 + - - +
358A PHE* 3.9 7.9 - + + -
390A ILE* 5.6 0.4 - - + -
391A GLN 3.4 13.5 - - - +
392A LEU* 3.8 5.2 - - + -
465A PHE 3.5 3.1 + - - -
466A ASP 2.9 28.1 + - - -
469A ILE* 3.7 26.4 - - + +
584A PRO* 3.3 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS 4.8 2.9 + - - -
276A ILE 5.4 1.3 + - - -
277A ARG* 4.0 24.7 + - - +
336A ILE* 6.0 0.3 - - - +
351A HIS 3.2 9.0 - - - -
352A LEU* 3.5 22.8 - - - +
353A ARG 5.2 0.2 + - - -
356A TYR* 1.3 78.5 + - - +
358A PHE* 1.3 61.8 + - - +
359A ASN* 4.3 16.4 - - - -
389A ASN 3.5 2.9 - - - +
390A ILE* 3.6 2.8 - - - +
391A GLN* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A HIS* 2.9 32.1 + - + +
356A TYR* 3.9 16.8 - - + -
357A SER* 1.3 73.4 - - - +
359A ASN* 1.3 63.0 + - - +
360A VAL* 3.7 23.1 - - + -
388A THR* 3.7 25.4 - - + -
389A ASN 3.4 3.8 - - - -
390A ILE* 3.4 35.7 - - + -
462A TRP* 4.0 2.7 - + - -
464A PHE* 3.5 15.1 - + - -
469A ILE* 3.8 39.5 - - + -
471A CYS* 4.1 11.7 - - - -
580A TYR* 5.6 0.7 - + - -
582A VAL* 4.0 20.0 - - + -
584A PRO* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS 4.8 7.9 + - - -
275A ALA* 4.9 2.4 + - - +
282A ASP* 3.1 32.1 + - - +
284A ASN* 3.3 4.4 + - - -
348A TYR* 3.9 9.2 + - + -
349A VAL 3.1 11.2 - - - +
350A GLN* 3.2 13.5 - - - +
351A HIS 3.1 23.7 + - - +
352A LEU* 4.0 3.8 - - - +
357A SER* 4.3 11.1 - - - -
358A PHE* 1.3 78.2 + - - +
360A VAL* 1.3 63.6 + - - +
388A THR* 3.5 1.9 - - - -
389A ASN* 2.8 49.8 + - - +
391A GLN* 4.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 3.3 8.0 - - - -
349A VAL* 2.9 45.3 + - + +
358A PHE* 3.7 25.6 - - + -
359A ASN* 1.3 77.3 - - - +
361A ARG* 1.3 66.2 + - - +
362A MET* 4.0 5.9 - - + +
386A GLY* 3.9 8.7 - - - +
387A ALA 3.2 8.1 - - - +
388A THR* 3.9 7.4 - - + -
462A TRP* 3.8 42.4 - - + -
464A PHE* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN* 4.1 11.7 + - - +
229A LEU* 3.8 38.6 + - + +
283A PHE 5.6 0.6 + - - -
284A ASN* 3.2 51.7 + - + +
287A GLY* 5.0 8.9 + - - +
347A ASP 4.1 3.1 - - - +
348A TYR* 4.3 2.2 - - + -
360A VAL* 1.3 74.0 - - - +
362A MET* 1.3 71.6 + - - +
368A ARG 3.9 19.8 + - - -
370A SER* 3.9 30.5 + - - +
383A LEU* 4.0 22.1 - - - +
384A SER* 3.3 17.6 + - - +
386A GLY* 2.9 27.5 + - - -
387A ALA 3.0 9.1 + - - +
----------------------------------------------------------
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