Contacts of the strand formed by residues 439 - 445 (chain A) in PDB entry 3HIG
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 439 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 3.6 25.6 - + + -
432A ASN 3.3 13.0 - - - +
434A ASN* 3.7 11.8 + - - +
438A GLY* 1.3 75.9 - - - +
440A ASN* 1.3 63.3 + - - +
441A PHE* 3.3 21.5 - - - -
442A TYR* 3.4 16.2 - - + -
716A VAL* 3.5 14.6 - - + -
718A PRO* 3.5 41.3 - - + +
724A ASN* 3.7 31.0 - - - -
744B TYR* 4.0 13.7 - + - -
745B ASN 4.0 1.6 - - - -
746B GLY* 3.7 22.9 - - - -
747B THR* 5.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ASN* 2.7 33.4 + - - +
433A SER 3.4 18.4 + - - -
434A ASN* 3.9 13.2 - - - +
439A PHE* 1.3 77.4 - - - +
441A PHE* 1.3 71.7 + - + +
717A TRP* 3.6 9.2 - - - -
718A PRO* 3.1 21.6 - - - +
206B TYR* 3.4 29.5 + - - -
210B TYR* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A HIS* 4.0 17.9 - + - -
431A PHE 3.9 0.2 - - - -
432A ASN* 2.9 52.4 + - + -
439A PHE* 3.3 14.1 - - - -
440A ASN* 1.3 88.1 - - + +
442A TYR* 1.3 69.9 + - - +
443A ALA* 3.8 20.2 - - + -
715A ILE* 4.1 8.3 - - + -
716A VAL 3.2 15.5 - - - +
717A TRP* 3.8 25.8 - + + -
208B GLU* 4.0 24.2 - - + -
209B GLY 4.2 6.1 - - - -
285B HIS* 4.4 7.6 - - + -
484B TYR* 3.7 20.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 3.7 23.6 - - - +
430A HIS 3.5 16.2 - - - -
431A PHE* 4.4 4.9 - - + -
439A PHE* 3.4 4.1 - - + -
441A PHE* 1.3 75.1 - - - +
443A ALA* 1.3 80.5 + - - +
444A GLY* 3.7 4.7 - - - -
714A VAL 4.6 2.0 - - - -
715A ILE* 3.2 5.2 - - - +
716A VAL* 2.8 46.7 + - + -
386B ALA* 3.4 19.7 - - + +
389B ILE* 3.3 26.3 - - + +
390B ASP* 2.8 39.5 + - - -
744B TYR* 3.6 39.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 3.2 2.2 - - - -
430A HIS 2.9 34.2 + - - +
441A PHE* 3.8 14.1 - - + -
442A TYR* 1.3 82.7 - - - +
444A GLY* 1.3 58.0 + - - +
714A VAL 3.4 8.3 - - - +
715A ILE* 4.1 7.6 - - + -
285B HIS* 3.5 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ARG* 3.4 11.7 - - - -
429A ARG* 4.1 0.4 - - - -
442A TYR* 3.7 5.8 - - - -
443A ALA* 1.3 76.3 - - - +
445A LEU* 1.3 60.5 + - - -
712A ASP 4.4 0.5 - - - +
713A THR* 3.6 5.6 - - - +
714A VAL* 2.9 35.9 + - - +
285B HIS* 5.3 1.6 - - - -
389B ILE* 3.7 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PRO* 3.5 4.9 - - - +
427A LEU* 2.9 42.8 + - + -
428A ARG* 3.0 46.3 + - + +
444A GLY* 1.3 73.8 - - - +
446A LYS* 1.3 71.3 + - - +
471A PRO* 5.6 2.7 - - + -
707A SER* 3.8 18.8 - - - +
710A SER* 3.6 17.3 - - - +
712A ASP* 3.5 34.8 - - + +
713A THR* 3.7 14.4 - - - +
389B ILE* 3.9 2.7 - - - +
----------------------------------------------------------
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