Contacts of the helix formed by residues 611 - 621 (chain A) in PDB entry 1ILE
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 ALA 611 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.7 6.5 + - - -
136A ARG* 3.2 40.2 - - - +
137A ILE* 3.7 16.4 - - + +
138A ALA 4.7 0.2 - - - +
606A ILE* 3.8 17.4 - - + +
610A GLY* 1.3 70.1 - - - -
612A ASP* 1.3 63.9 + - - +
613A ALA 3.0 1.2 + - - -
614A LEU* 3.0 14.6 + - - +
615A ARG* 3.2 17.0 + - + +
760A PHE* 3.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.4 13.8 + - - +
610A GLY 3.3 0.8 + - - -
611A ALA* 1.3 78.1 - - - +
613A ALA* 1.3 56.0 + - - +
615A ARG* 3.2 8.0 - - - +
616A TRP* 2.8 29.6 + - - +
643A PHE* 3.9 10.3 - - + -
758A THR* 3.0 29.2 - - + +
759A PRO* 3.3 20.8 - - - +
760A PHE* 3.0 27.0 - - - +
761A LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ILE* 5.2 0.2 - - + -
609A PHE* 3.5 32.1 + - + +
610A GLY 2.9 13.2 + - - +
612A ASP* 1.3 76.0 - - - +
614A LEU* 1.3 68.3 + - - +
615A ARG 3.2 0.7 - - - -
616A TRP* 3.9 1.6 - - - +
617A TYR* 2.8 25.6 + - - +
635A VAL* 4.3 11.5 - - + +
638A THR* 5.3 1.6 + - - -
639A VAL* 4.6 7.9 - - + -
643A PHE* 4.0 16.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 5.0 2.9 - - + -
58A ALA* 4.2 24.2 - - + -
62A SER* 5.9 0.2 - - - +
137A ILE* 5.0 7.4 - - + -
602A PRO* 3.6 34.8 - - + +
605A ILE* 4.2 13.5 - - + +
606A ILE* 3.8 21.5 - - + -
610A GLY 3.6 2.0 + - - -
611A ALA* 3.0 10.4 + - - +
613A ALA* 1.3 79.3 - - - +
615A ARG* 1.3 68.1 + - + +
617A TYR* 2.9 12.1 + - - +
618A ILE* 3.0 27.6 + - + +
630A PHE* 3.6 33.4 - - + -
635A VAL* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 4.5 21.1 + - - +
65A ASP* 2.8 37.3 + - - +
66A LEU 4.6 0.4 - - - +
137A ILE* 5.2 7.9 - - + +
138A ALA* 3.0 45.1 + - - +
139A TYR* 4.6 0.4 - - - +
611A ALA* 3.4 15.8 - - + +
612A ASP* 3.2 11.6 + - - +
614A LEU* 1.3 82.7 - - + +
616A TRP* 1.3 65.5 + - - +
618A ILE* 3.1 4.1 + - - +
619A TYR* 3.0 48.3 + - + -
756A PRO 3.3 22.0 + - - -
757A PHE 3.2 13.6 + - - +
759A PRO* 3.5 18.2 - - - +
760A PHE* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ASP 2.8 20.6 + - - +
613A ALA 3.9 2.9 - - - +
615A ARG* 1.3 73.1 - - - +
617A TYR* 1.3 65.7 + - - +
619A TYR* 3.0 15.8 + + - +
620A VAL* 3.1 37.7 + - + +
638A THR* 4.5 15.8 - - - +
642A TYR* 3.6 43.2 - + + +
643A PHE* 3.7 22.0 - + + -
704A ALA* 3.2 46.9 - - + -
707A LEU* 4.2 9.4 - - + -
708A ARG* 3.7 22.7 - - + +
754A ALA* 6.0 1.6 - - + -
757A PHE* 3.9 28.7 - + + -
758A THR* 4.1 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA 2.8 17.5 + - - +
614A LEU* 2.9 8.5 + - - +
616A TRP* 1.3 73.7 - - - +
618A ILE* 1.3 67.9 + - + +
620A VAL* 4.1 4.0 - - - -
621A SER* 2.8 56.7 + - - -
628A ARG* 4.4 5.5 - - + +
629A ARG* 2.8 37.4 + - - -
630A PHE* 3.6 32.3 - + + -
634A LEU* 4.1 25.3 - - + +
635A VAL* 4.4 19.3 - - + -
638A THR* 4.0 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 4.0 20.6 - - + -
62A SER* 4.2 18.4 - - - +
63A TYR* 3.4 33.9 + - + +
584A ILE* 4.7 20.0 - - + -
614A LEU* 3.0 34.7 + - + +
615A ARG 3.4 6.3 - - - +
617A TYR* 1.3 87.9 - - + +
619A TYR* 1.3 65.2 + - + +
621A SER* 3.0 19.5 + - - -
622A ALA 3.8 7.4 - - - +
628A ARG* 3.8 8.5 + - - -
630A PHE* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 2.8 46.8 + - - -
63A TYR* 4.3 13.7 - + - -
66A LEU* 3.5 31.0 - - + +
615A ARG* 3.0 34.7 + - + -
616A TRP* 3.0 11.2 + + + +
618A ILE* 1.3 79.7 - - - +
620A VAL* 1.3 57.9 + - + +
700A PRO* 4.1 11.4 - - + +
701A THR* 2.8 39.5 - - - +
704A ALA* 3.8 18.2 - - + -
756A PRO 4.6 0.2 + - - -
757A PHE* 3.5 42.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A TRP* 3.1 48.8 + - + +
617A TYR* 3.6 6.3 - - - +
619A TYR* 1.3 77.0 - - + +
621A SER* 1.3 69.4 + - - +
622A ALA 3.3 2.5 - - - -
638A THR* 4.5 13.9 - - + -
701A THR 5.1 0.2 - - - -
704A ALA* 5.1 1.8 - - + -
705A ARG* 2.7 52.4 + - + +
708A ARG* 5.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A TYR* 2.8 50.7 + - - -
618A ILE* 3.0 14.7 + - - -
620A VAL* 1.3 72.8 - - - +
622A ALA* 1.3 70.0 + - - +
628A ARG* 3.0 23.9 + - - -
629A ARG* 6.2 0.2 - - - -
705A ARG* 3.0 10.6 + - - -
----------------------------------------------------------
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