Contacts of the strand formed by residues 439 - 445 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A TYR* 3.9 14.4 - + - -
745A ASN 4.0 1.8 - - - -
746A GLY* 3.6 26.5 - - - -
747A THR* 5.4 2.2 - - + -
431B PHE* 3.6 24.5 - + + -
432B ASN 3.4 11.2 - - - +
434B ASN* 3.7 10.7 + - - +
438B GLY* 1.3 75.9 - - - +
440B ASN* 1.3 61.9 + - - +
441B PHE* 3.3 22.0 - - - +
442B TYR 3.5 5.2 - - - -
716B VAL* 3.4 40.4 - - + -
718B PRO* 3.4 37.6 - - + +
724B ASN* 3.8 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TYR* 3.1 31.3 + - - -
210A TYR* 4.7 1.4 - - - -
432B ASN* 2.8 32.6 + - - +
433B SER 3.6 16.4 + - - -
434B ASN* 4.0 12.5 - - - +
439B PHE* 1.3 75.5 - - - +
441B PHE* 1.3 70.3 + - + +
717B TRP* 3.7 8.8 - - - -
718B PRO* 3.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 4.2 23.6 - - + -
209A GLY 4.4 5.6 - - - -
285A HIS* 4.2 9.2 - - + -
484A TYR* 3.8 20.2 - - - -
430B HIS* 4.1 16.6 - + - -
431B PHE* 4.0 0.3 - - - -
432B ASN* 3.0 54.3 + - + -
439B PHE* 3.3 14.4 - - - -
440B ASN* 1.3 85.6 - - + +
442B TYR* 1.3 71.2 + - - +
443B ALA* 3.8 19.5 - - + -
715B ILE* 4.0 9.0 - - + -
716B VAL 3.2 15.9 - - - +
717B TRP* 3.8 26.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ALA* 3.7 18.1 - - + +
389A ILE* 3.3 25.9 - - + +
390A ASP* 2.7 40.5 + - - -
744A TYR* 3.7 39.3 - + + +
429B ARG* 3.7 19.8 - - - +
430B HIS 3.4 15.0 - - - -
431B PHE* 4.5 4.0 - - + -
439B PHE* 3.5 3.7 - - + -
441B PHE* 1.3 75.3 - - - +
443B ALA* 1.3 70.3 + - - +
444B GLY* 3.6 18.9 - - - -
714B VAL 4.5 2.0 - - - -
715B ILE* 3.3 3.3 - - - +
716B VAL* 2.8 47.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A HIS* 3.4 45.5 - - + +
429B ARG* 3.1 3.0 - - - -
430B HIS 2.8 32.5 + - - +
441B PHE* 3.8 13.2 - - + -
442B TYR* 1.3 82.8 - - - +
444B GLY* 1.3 59.1 + - - +
713B THR* 5.3 0.2 - - + -
714B VAL 3.4 5.2 - - - +
715B ILE* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A HIS* 5.1 1.1 - - - -
389A ILE* 3.7 10.5 - - - +
428B ARG* 3.4 11.0 - - - -
429B ARG* 4.1 0.2 - - - -
442B TYR* 3.6 18.6 - - - -
443B ALA* 1.3 76.2 - - - +
445B LEU* 1.3 60.4 + - - -
446B LYS 4.4 0.2 + - - -
712B ASP 4.6 0.3 - - - +
713B THR* 3.5 6.6 - - - +
714B VAL* 3.0 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 3.7 3.8 - - - +
426B PRO* 3.3 3.6 - - - +
427B LEU* 2.8 39.9 + - + -
428B ARG* 2.9 52.7 + - + +
444B GLY* 1.3 74.8 - - - +
446B LYS* 1.3 75.7 - - - +
471B PRO* 5.6 4.0 - - + -
707B SER* 4.0 15.5 - - - +
710B SER* 3.6 14.4 - - - +
712B ASP* 3.5 33.4 - - + +
713B THR* 3.5 14.8 - - - +
----------------------------------------------------------
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