Contacts of the helix formed by residues 622 - 632 (chain D) in PDB entry 1FVU
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 HIS 622 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ASP* 4.1 9.7 + - - -
496B TYR* 3.8 31.5 - + - -
621D MET* 1.3 75.2 - - - +
623D TRP* 1.3 66.8 + - - +
624D ASP* 4.4 6.5 - - + +
625D ASP* 3.1 20.6 + - - +
626D ALA* 2.9 19.4 + - - +
713D CYS 3.7 4.3 - - - +
714D THR* 2.7 41.1 + - + +
715D ARG 3.4 6.1 - - - -
716D PHE* 3.0 43.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 623 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 4.1 12.1 - - - -
622D HIS* 1.3 69.9 - - - +
624D ASP* 1.3 83.6 + - - +
626D ALA* 3.1 2.1 + - - +
627D GLU* 2.9 44.9 + - + -
639D LEU* 3.2 21.4 - - + +
665D TRP* 3.5 42.4 - + + +
666D ILE 2.9 21.1 + - - -
667D GLY* 4.0 6.3 - - - -
668D LEU 3.6 17.1 + - - -
669D SER* 3.4 31.6 - - - -
696D TYR* 3.8 7.4 - - - -
698D CYS* 3.4 23.1 - - + -
713D CYS* 3.0 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 624 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B HIS* 3.6 17.8 + - - -
425B ASP* 4.7 3.6 - - - +
622D HIS* 3.3 4.8 - - + +
623D TRP* 1.3 89.0 - - - +
625D ASP* 1.3 62.5 + - - +
627D GLU* 3.5 2.5 + - - +
628D GLU* 3.0 29.7 + - - +
696D TYR* 2.6 43.3 + - - -
713D CYS 4.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 625 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D MET* 3.7 25.4 - - + +
622D HIS* 3.1 24.5 + - - +
624D ASP* 1.3 78.7 - - - +
626D ALA* 1.3 61.8 + - - +
628D GLU* 3.8 16.1 - - - +
629D PHE* 2.8 31.2 + - - +
716D PHE* 6.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 626 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D MET* 4.0 12.3 - - + -
622D HIS 2.9 11.7 + - - +
623D TRP 3.5 7.4 - - - +
625D ASP* 1.3 74.7 - - - +
627D GLU* 1.3 66.1 + - - +
629D PHE* 3.2 3.8 + - - +
630D CYS* 2.9 27.4 + - - -
639D LEU* 4.1 9.0 - - + -
665D TRP* 4.0 14.4 - - + -
719D PHE* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 2.9 32.1 + - - +
623D TRP* 2.9 37.5 + - + +
624D ASP 3.7 3.8 - - - +
626D ALA* 1.3 75.8 - - - +
628D GLU* 1.3 65.7 + - - +
630D CYS* 3.1 13.8 + - - +
631D THR* 3.2 21.6 + - + +
638D HIS* 2.7 31.6 + - - -
639D LEU* 3.2 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624D ASP 3.0 19.8 + - - +
625D ASP* 3.8 16.2 - - - +
627D GLU* 1.3 77.5 - - - +
629D PHE* 1.3 64.2 + - - +
631D THR* 2.6 28.3 + - - +
632D GLU* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617D PHE* 3.4 34.5 - + - -
619D GLU* 4.0 16.6 - - + -
621D MET* 3.9 23.1 - - + -
625D ASP 2.8 22.3 + - - +
626D ALA 3.4 3.8 - - - +
628D GLU* 1.3 74.8 + - - +
630D CYS* 1.3 63.1 + - - +
632D GLU* 3.1 16.6 + - + +
633D GLN* 3.1 55.7 - - + +
719D PHE* 3.4 24.5 - + - -
721D CYS* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626D ALA 2.9 18.0 + - - -
627D GLU 3.1 9.2 + - - +
629D PHE* 1.3 75.4 - - - +
631D THR* 1.3 60.5 + - - +
632D GLU 3.4 0.3 + - - -
633D GLN* 3.4 12.2 + - - +
637D ALA* 3.1 22.5 - - - +
638D HIS* 3.6 25.6 - - - +
639D LEU* 3.9 9.4 - - - +
719D PHE* 3.9 9.2 - - - -
721D CYS* 2.0 56.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627D GLU* 3.2 31.9 - - + +
628D GLU* 2.6 23.0 + - - +
630D CYS* 1.3 76.3 - - - +
632D GLU* 1.3 62.9 + - - +
633D GLN 3.3 1.3 - - - -
634D GLN 3.5 16.3 - - - +
635D THR* 5.0 2.3 - - - -
636D GLY* 5.1 1.7 + - - +
637D ALA 3.2 20.4 - - - +
638D HIS* 3.9 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D GLU* 3.1 34.9 + - - +
629D PHE* 3.1 12.2 + - + +
631D THR* 1.3 84.5 + - - +
633D GLN* 1.3 68.3 + - - +
634D GLN 3.8 0.2 - - - -
----------------------------------------------------------
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