Contacts of the helix formed by residues 733 - 742 (chain D) in PDB entry 7KHI
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 SER 733 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726D ALA* 5.4 4.3 - - - -
732D GLY* 1.3 74.3 - - - -
734D ALA* 1.3 66.6 + - - +
735D ALA* 3.3 9.2 + - - +
736D GLN* 2.5 43.3 + - - +
737D ILE* 3.1 14.4 + - - +
65M GLU* 2.7 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 734 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D SER* 5.2 1.8 + - - +
698D MET* 4.1 27.0 - - + +
726D ALA* 5.7 1.9 - - - +
733D SER* 1.3 74.8 - - - +
735D ALA* 1.3 57.9 + - - +
737D ILE* 3.4 4.7 + - - +
738D ARG* 2.8 35.5 + - - +
61M HIS* 5.4 8.3 - - + +
65M GLU* 4.5 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 735 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733D SER* 3.0 10.7 + - - +
734D ALA* 1.3 78.5 - - - +
736D GLN* 1.3 67.0 + - - +
738D ARG* 3.0 45.9 + - - +
739D GLN* 3.0 16.2 + - - +
61M HIS* 4.3 18.7 + - + +
81M GLU* 5.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 736 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104C PRO 4.2 15.9 - - - +
1105C SER* 4.8 15.3 + - - +
1107C MET* 4.5 21.5 - - + -
732D GLY* 4.3 7.7 - - - -
733D SER* 2.5 63.4 + - - +
735D ALA* 1.3 73.2 - - + +
737D ILE* 1.3 66.8 + - + +
739D GLN* 2.9 12.8 + - - +
740D LEU* 2.8 22.3 + - - +
65M GLU* 4.3 4.6 + - - -
69M PHE* 6.0 2.6 - - - -
78M GLN* 5.3 14.6 - - - +
81M GLU* 6.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104C PRO* 5.0 6.5 - - + -
697D MET* 3.6 26.8 - - + +
698D MET* 3.8 13.2 - - + -
701D LEU* 3.8 14.8 - - + -
722D ILE* 3.2 50.7 - - + +
723D TYR* 5.6 0.7 - - - -
726D ALA* 4.2 18.8 - - + -
732D GLY* 5.8 2.7 - - - -
733D SER 3.1 12.4 + - - +
734D ALA* 3.6 8.5 - - - +
736D GLN* 1.3 75.8 - - + +
738D ARG* 1.3 63.2 + - - +
740D LEU* 3.2 5.4 + - + +
741D ALA* 2.9 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 738 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690D ASN* 3.9 20.5 + - - +
691D ASP* 5.6 1.6 - - - +
694D SER* 2.9 42.6 + - - +
697D MET* 3.4 11.4 - - + +
734D ALA* 2.8 19.4 + - - +
735D ALA* 3.0 47.0 + - - +
737D ILE* 1.3 76.7 - - - +
739D GLN* 1.3 61.8 + - + +
742D GLY* 2.4 40.6 + - - -
743D MET 4.0 12.8 - - - +
744D ARG* 5.6 1.1 - - - +
61M HIS* 5.1 9.9 + - - -
81M GLU* 5.5 3.2 + - - -
85M GLU* 5.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107C MET* 2.8 46.8 - - - +
735D ALA* 3.0 15.1 + - - +
736D GLN* 2.9 9.5 + - - +
738D ARG* 1.3 83.4 - - + +
740D LEU* 1.3 62.1 + - - +
742D GLY 4.2 0.5 - - - +
744D ARG* 3.6 53.4 + - + +
747D MET* 5.8 1.8 - - - +
762D ASN* 4.1 5.9 - - - +
763D PHE* 3.6 25.9 + - + -
81M GLU* 4.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 740 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103C VAL* 5.4 0.9 - - + +
1104C PRO* 3.7 29.2 - - + +
1107C MET* 4.5 14.8 - - + -
1109C ILE* 3.8 31.2 - - + -
644D MET* 3.8 20.9 - - + -
722D ILE* 4.3 17.0 - - + -
736D GLN 2.8 36.0 + - - +
737D ILE* 3.8 9.6 - - + +
739D GLN* 1.3 78.6 - - - +
741D ALA* 1.3 60.4 + - + +
762D ASN* 3.2 20.1 - - - +
763D PHE* 4.6 14.1 - - + -
764D ARG* 3.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 741 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D MET* 4.7 10.3 - - + -
645D VAL 3.9 21.8 - - - +
646D ILE* 4.1 4.7 - - - +
647D PRO* 3.5 18.9 - - - +
650D LYS* 5.3 1.2 - - - +
697D MET* 3.7 23.6 - - + -
701D LEU* 5.2 3.1 - - + -
737D ILE* 2.9 18.1 + - + +
740D LEU* 1.3 74.8 - - + +
742D GLY* 1.3 60.4 + - - +
762D ASN* 3.6 16.0 + - - +
764D ARG* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 742 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D PRO* 5.2 0.9 - - - -
650D LYS* 4.7 6.3 - - - -
693D VAL* 4.8 11.2 - - - -
694D SER* 5.7 0.7 - - - -
697D MET* 4.3 8.7 - - - +
738D ARG* 2.4 36.2 + - - +
739D GLN 4.2 0.9 - - - +
741D ALA* 1.3 68.6 - - - +
743D MET* 1.3 64.8 + - - -
744D ARG 3.7 0.5 + - - -
762D ASN* 3.0 27.5 - - - +
----------------------------------------------------------
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