Contacts of the helix formed by residues 638 - 647 (chain A) in PDB entry 1TAQ
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 ILE 638 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLN* 3.7 25.7 - - - +
616A LEU* 4.0 14.1 - - + -
628A LEU* 3.7 29.4 - - + -
631A VAL* 3.8 33.9 - - + -
632A PHE* 4.2 19.1 - - + -
636A ARG 3.0 7.1 + - - -
637A ASP* 1.3 70.7 + - - +
639A HIS* 1.3 70.2 + - + +
641A GLU* 4.6 0.4 - - - -
642A THR* 2.5 47.6 + - - +
666A ASN* 3.4 15.7 - - - +
700A PHE* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLN* 4.0 16.2 + - + -
616A LEU* 4.5 5.9 - - + +
637A ASP* 2.9 9.0 + - - +
638A ILE* 1.3 91.8 - - + +
640A THR* 1.3 65.3 + - - +
642A THR 4.1 0.2 - - - -
643A ALA* 3.3 7.3 + - - +
659A ARG* 3.5 44.4 + - + +
662A ALA* 3.1 24.1 - - - +
663A LYS* 3.2 50.7 + - + +
666A ASN* 3.4 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ASP* 2.9 29.9 + - - +
639A HIS* 1.3 76.0 - - - +
641A GLU* 1.3 61.6 + - - +
643A ALA* 2.8 9.7 + - - +
644A SER* 2.8 27.5 + - - -
651A ARG* 3.6 36.6 - - + +
654A VAL* 3.7 12.7 - - + +
659A ARG* 3.4 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A VAL* 3.9 24.9 - - + -
634A GLU* 4.6 1.4 - - - +
636A ARG* 3.6 26.6 - - + +
637A ASP 3.0 17.0 + - - +
638A ILE 4.2 2.5 - - - +
640A THR* 1.3 77.2 - - - +
642A THR* 1.3 63.6 + - - +
644A SER* 2.9 17.8 + - - -
645A TRP* 3.1 42.6 + - + -
651A ARG* 2.8 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ILE* 2.5 35.4 + - - +
641A GLU* 1.3 75.9 - - - +
643A ALA* 1.3 62.3 + - - +
645A TRP* 3.6 5.2 + - - +
646A MET* 3.1 35.2 + - + +
662A ALA* 4.0 12.6 - - + -
666A ASN* 3.1 16.2 + - - +
696A TYR* 3.7 33.7 - - + -
699A SER* 5.3 1.0 + - - +
700A PHE* 3.9 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A HIS 3.3 13.9 + - - +
640A THR 2.8 12.4 + - - +
642A THR* 1.3 78.6 - - - +
644A SER* 1.3 54.8 + - - +
646A MET* 4.4 0.4 - - - -
647A PHE* 2.8 44.1 + - - +
649A VAL* 4.7 0.9 - - - +
654A VAL* 3.3 28.5 - - + -
658A MET* 3.9 20.1 - - + +
662A ALA* 3.8 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A THR 2.8 7.4 + - - -
641A GLU* 3.1 14.8 - - - -
643A ALA* 1.3 75.3 - - - +
645A TRP* 1.3 68.7 - - - +
648A GLY* 2.7 37.9 + - - -
649A VAL* 2.8 24.8 + - - +
650A PRO* 3.4 0.5 - - - +
651A ARG* 2.9 29.8 + - - +
654A VAL* 4.0 3.0 - - - +
833A BGL 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASN* 3.7 37.9 - - + -
630A ARG* 4.3 31.1 - - + +
631A VAL* 3.7 24.5 - - + -
634A GLU* 5.7 1.6 - - - -
641A GLU* 3.1 34.7 + - + +
642A THR 3.9 3.4 - - - +
644A SER* 1.3 87.8 - - - +
646A MET* 1.3 57.5 + - - +
695A ARG* 4.8 2.8 - - - +
699A SER* 3.9 28.0 + - - -
700A PHE* 4.1 19.3 - + - -
833A BGL 3.4 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A THR* 3.1 38.2 + - + +
645A TRP* 1.3 79.4 - - - +
647A PHE* 1.3 85.8 + - + +
648A GLY 3.5 1.1 - - - -
661A ALA* 5.3 1.3 - - + -
662A ALA* 4.7 5.8 - - - -
665A ILE* 3.5 26.2 - - + -
692A PHE* 3.2 37.5 - - + +
695A ARG* 2.7 57.3 + - + +
696A TYR* 4.1 12.8 - - - +
699A SER* 4.5 1.8 - - - +
833A BGL 3.6 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ALA* 2.8 21.8 + - - +
644A SER 3.6 0.4 - - - -
646A MET* 1.3 106.7 - - + +
648A GLY* 1.3 66.6 + - - +
649A VAL* 3.2 11.7 - - + +
658A MET* 3.5 60.9 - - + +
661A ALA* 4.2 7.6 - - + -
662A ALA 5.1 0.2 - - - -
692A PHE* 3.5 42.2 - + - -
695A ARG* 3.9 15.5 - - - +
833A BGL 4.2 2.9 - - - -
----------------------------------------------------------
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