Contacts of the helix formed by residues 708 - 720 (chain A) in PDB entry 5I4E
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 GLU 708 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A PRO 2.8 17.5 + - - +
699A ASN* 3.7 21.8 - - + +
700A HIS 5.4 0.6 + - - +
701A GLU* 3.4 21.5 - - - +
706A LYS* 3.8 17.1 + - + +
707A LEU* 1.4 73.8 - - - +
709A PRO* 1.4 73.3 - - - +
710A ARG 3.4 2.5 - - - +
711A LEU* 3.1 15.3 + - + +
712A VAL* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU 3.4 25.6 - - - +
63A HIS* 3.4 30.1 - - - +
64A GLY* 4.0 4.0 - - - +
122A LEU* 4.3 8.1 - - + +
126A ARG* 4.1 18.6 - - - +
707A LEU* 3.3 21.1 - - + +
708A GLU* 1.4 85.6 - - + +
710A ARG* 1.3 56.1 + - - +
712A VAL* 3.4 1.9 + - - +
713A LEU* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER 3.0 26.9 + - - -
61A GLU* 3.4 39.1 + - - +
62A LEU 5.8 0.7 - - - +
64A GLY* 4.0 10.1 + - - +
708A GLU* 3.4 1.2 - - - +
709A PRO* 1.3 78.6 - - + +
711A LEU* 1.3 61.6 + - - +
713A LEU* 3.6 17.2 + - - +
714A ASP* 3.2 43.6 + - - +
717A ARG* 4.8 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 4.2 9.0 - - - +
697A VAL* 3.9 5.4 - - + +
698A PRO 3.7 2.9 - - - +
699A ASN* 3.5 42.6 - - - +
700A HIS* 3.5 38.4 - - + +
708A GLU* 3.1 17.2 + - + +
710A ARG* 1.3 75.5 - - - +
712A VAL* 1.4 63.8 + - - +
714A ASP* 3.4 11.7 + - + +
715A GLN* 3.0 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.4 12.1 - - + -
125A LEU* 4.7 10.5 - - + -
145A ILE* 5.4 4.7 - - + -
696A ILE* 3.9 22.7 - - + -
697A VAL 4.0 10.1 - - - +
698A PRO* 4.1 6.7 - - + +
707A LEU* 3.7 34.3 - - + -
708A GLU 3.1 10.1 + - - +
709A PRO* 3.9 3.8 - - + +
711A LEU* 1.4 71.1 - - - +
713A LEU* 1.3 61.4 + - - +
715A GLN* 3.4 7.8 + - - +
716A LEU* 3.0 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY* 4.1 20.4 - - - +
65A PHE* 4.0 17.0 - - + -
118A GLU* 4.6 11.2 - - + +
122A LEU* 3.6 33.0 - - + -
709A PRO 2.9 25.5 + - - +
710A ARG* 3.8 22.4 - - - +
711A LEU 3.4 0.2 - - - -
712A VAL* 1.3 77.7 - - - +
714A ASP* 1.3 60.1 + - - +
716A LEU* 3.5 12.4 + - + +
717A ARG* 3.1 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ARG* 3.2 26.6 + - - +
711A LEU* 3.6 14.3 - - + +
712A VAL 3.3 0.2 - - - -
713A LEU* 1.3 75.8 - - - +
715A GLN* 1.3 59.0 + - + +
717A ARG* 3.3 23.8 + - - +
718A CYS* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 3.8 26.9 + - + +
695A CYS 4.2 2.1 - - - +
696A ILE* 3.3 25.8 - - + +
697A VAL* 2.8 50.8 + - - +
711A LEU* 3.0 34.8 + - + +
712A VAL 3.6 5.4 - - - +
713A LEU 3.3 0.4 - - - -
714A ASP* 1.3 77.2 - - + +
716A LEU* 1.3 65.1 + - - +
718A CYS* 3.4 9.4 + - - -
719A ASN* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 5.4 1.6 - - + +
121A VAL* 4.2 14.1 - - + -
122A LEU* 4.8 6.3 - - - +
125A LEU* 3.8 28.5 - - + -
143A VAL* 4.8 3.6 - - + -
696A ILE* 4.5 15.9 - - + -
712A VAL* 3.0 37.8 + - + +
713A LEU* 3.8 18.4 - - + +
715A GLN* 1.3 74.9 - - - +
717A ARG* 1.4 59.5 + - - +
720A GLY* 3.4 2.4 + - - -
721A VAL* 3.1 60.2 + - + +
722A LEU* 4.4 7.5 + - + +
723A GLU* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 5.1 3.8 - - - -
118A GLU* 3.4 39.9 + - - +
532A LEU* 4.7 4.7 - - - +
710A ARG* 4.8 11.7 - - - +
713A LEU* 3.1 48.0 + - - +
714A ASP* 3.4 23.5 + - - +
715A GLN 3.1 0.2 - - - -
716A LEU* 1.4 74.5 - - + +
718A CYS* 1.4 64.0 + - - +
719A ASN 3.3 0.2 - - - -
720A GLY* 3.4 12.5 + - - -
723A GLU* 4.7 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLN* 3.5 19.4 + - - +
532A LEU* 4.7 6.4 - - - +
599A TYR* 3.3 37.3 - - + +
600A ALA* 4.0 23.8 - - - -
714A ASP 2.9 23.4 + - - +
715A GLN* 3.7 13.5 - - - -
717A ARG* 1.4 73.0 - - - +
719A ASN* 1.3 71.5 + - - +
720A GLY* 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A THR* 4.3 5.2 + - - -
198A GLY* 5.7 4.5 + - - -
503A GLN* 3.0 21.5 + - - +
506A PHE* 3.3 2.9 - - - -
599A TYR* 4.9 4.3 - - - -
694A ARG* 2.9 54.5 + - - +
695A CYS 4.7 3.2 + - - -
696A ILE* 3.5 25.5 - - - +
715A GLN* 3.0 23.6 + - - +
716A LEU 4.0 0.2 - - - +
718A CYS* 1.3 88.3 - - - +
720A GLY* 1.3 58.7 + - - +
721A VAL* 3.9 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PHE* 3.8 9.8 - - - -
511A PHE* 4.3 0.5 - - - -
532A LEU* 4.0 19.1 - - - -
716A LEU 3.4 3.8 + - - -
717A ARG 3.4 6.4 + - - -
718A CYS 3.3 3.8 - - - -
719A ASN* 1.3 79.6 - - - +
721A VAL* 1.3 64.6 + - - +
723A GLU* 3.2 20.9 + - - +
724A GLY* 3.0 19.6 + - - -
----------------------------------------------------------
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