Contacts of the helix formed by residues 703 - 708 (chain B) in PDB entry 1KT8
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 LEU 703 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PRO* 4.7 4.9 - - + -
571B SER 5.9 0.4 - - - +
573B GLN 3.8 6.7 - - - +
574B LEU* 3.9 2.7 - - + -
575B PHE* 4.2 0.7 - - - -
603B SER* 3.8 21.8 - - - +
606B ARG* 4.6 2.9 - - + -
607B LEU* 3.8 42.2 - - + -
698B VAL* 3.8 35.0 - - + -
701B TYR* 3.1 29.3 + - + +
702B LYS* 1.3 74.7 - - - +
704B GLY* 1.3 66.7 + - - +
705B GLY* 4.1 7.0 - - - +
706B ASN* 3.0 21.3 + - - +
707B TYR* 3.3 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS 3.3 25.6 - - - -
70A TYR 3.5 14.6 - - - +
71A SER* 3.6 7.2 - - - -
573B GLN* 3.4 25.7 + - - -
575B PHE* 4.1 6.6 - - - -
702B LYS 4.0 1.8 + - - -
703B LEU* 1.3 70.7 - - - +
705B GLY* 1.3 56.0 + - - +
707B TYR* 2.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.6 16.7 - - - -
205A GLY* 4.2 16.4 - - - -
571B SER* 3.6 12.5 + - - -
703B LEU* 3.0 6.8 + - - +
704B GLY* 1.3 75.9 - - - +
706B ASN* 1.3 62.6 + - - +
709B PRO* 3.1 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 5.9 3.8 - - - -
692B ARG* 4.5 31.9 + - - +
693B ALA* 5.5 0.8 - - - +
698B VAL* 2.9 40.2 + - - +
699B GLY* 4.0 9.2 - - - +
701B TYR 2.9 25.8 - - - +
703B LEU* 3.0 17.3 + - - +
705B GLY* 1.3 78.8 - - - +
707B TYR* 1.3 68.7 + - + +
709B PRO* 4.0 4.5 - - - +
710B THR* 3.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.9 21.5 - + + -
155A VAL* 4.4 22.1 - - + +
575B PHE* 3.5 28.3 - + - -
692B ARG* 4.8 3.4 + - - -
701B TYR 5.2 0.7 + - - -
702B LYS* 3.4 17.4 + - + +
703B LEU 3.3 26.5 - - - -
704B GLY 2.9 9.3 + - - +
706B ASN* 1.3 88.9 - - + +
708B GLY* 1.3 56.7 + - - +
709B PRO 3.3 2.2 - - - -
710B THR* 2.7 41.3 + - + -
711B VAL* 3.8 4.0 + - - +
740B THR* 4.2 8.1 - - + -
766B LEU* 4.7 3.5 - - - +
900B ILP 2.8 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.0 27.9 + - - -
71A SER* 4.5 2.9 - - - -
72A LEU* 3.9 14.8 - - - +
106A ARG* 4.9 0.3 + - - +
107A LEU* 3.5 18.6 - - - +
704B GLY 3.6 1.4 + - - -
707B TYR* 1.3 74.7 - - - +
709B PRO* 1.4 66.3 - - - +
710B THR 3.0 1.2 + - - -
711B VAL* 3.3 20.1 + - - +
712B LEU 4.8 0.3 + - - -
----------------------------------------------------------
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