Contacts of the helix formed by residues 686 - 705 (chain A) in PDB entry 2IVF
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 686 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A ALA* 4.2 7.6 - - + +
657A GLU 4.6 2.1 - - - +
658A LYS* 3.6 30.6 - - + +
659A HIS* 4.2 6.8 + - - -
676A ARG* 4.7 8.5 + - - -
680A PRO* 5.5 2.9 - - + +
685A ARG* 1.3 75.4 - - - +
687A GLU* 1.3 63.3 + - - +
688A TRP 4.4 1.3 - - - +
689A ASP* 3.2 13.9 + - + +
690A ALA* 2.9 25.9 + - - +
734A LEU 4.9 0.3 - - - +
735A THR* 3.5 14.8 - - - +
736A ASN* 2.9 53.2 + - - +
737A GLU 5.0 0.5 + - - -
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Residues in contact with GLU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA* 3.7 0.6 - - - +
199A ALA* 3.5 34.0 - - + +
606A LEU* 4.0 11.2 - - + -
635A LEU* 4.3 7.4 - - + -
652A CYS* 3.2 23.5 - - - +
653A ALA 4.5 0.2 - - - -
658A LYS* 2.9 28.8 + - - +
685A ARG 4.6 0.2 - - - -
686A GLU* 1.3 73.9 - - - +
688A TRP* 1.3 59.2 + - - +
690A ALA* 3.3 7.4 + - - +
691A ILE* 2.8 40.6 + - + +
736A ASN* 4.6 3.0 + - - -
1987A MD1 2.7 39.2 + - - +
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Residues in contact with TRP 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 3.8 13.5 - - + -
199A ALA* 5.0 1.4 - - - +
201A GLY 4.2 0.2 - - - -
202A ALA* 3.5 43.3 - - + +
205A ARG* 3.4 24.7 - - - -
491A LEU* 3.9 24.7 - - + -
686A GLU 3.3 0.4 - - - -
687A GLU* 1.3 78.6 - - - +
689A ASP* 1.3 50.5 + - - +
691A ILE* 3.8 0.2 - - - -
692A ALA* 2.7 37.2 + - + +
727A PHE* 3.4 37.0 - + - -
728A THR* 4.8 0.4 - - - +
733A LEU* 2.9 38.5 + - + -
734A LEU* 3.8 23.8 - - - -
735A THR 4.2 0.2 - - - -
736A ASN* 3.9 20.9 + - - +
739A CYS* 3.4 26.2 - - - -
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Residues in contact with ASP 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A ARG* 2.9 44.7 + - - +
686A GLU* 3.2 21.9 + - + +
688A TRP* 1.3 76.6 - - - +
690A ALA* 1.3 55.0 + - - +
692A ALA* 3.1 8.4 + - - +
693A LEU* 2.8 34.0 + - - +
734A LEU 4.0 19.3 + - - +
735A THR* 6.2 0.2 - - + -
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Residues in contact with ALA 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 3.7 35.2 - - + -
635A LEU* 4.0 19.3 - - + -
650A LEU* 5.0 1.1 - - + -
652A CYS* 5.2 2.9 - - - -
685A ARG* 4.5 6.0 - - + +
686A GLU 2.9 13.6 + - - +
687A GLU* 3.5 9.6 - - - +
689A ASP* 1.3 76.4 + - - +
691A ILE* 1.3 55.9 + - - +
693A LEU* 3.2 5.7 + - - +
694A ILE* 3.0 33.4 + - - +
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Residues in contact with ILE 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA 4.5 0.4 - - - +
202A ALA* 3.5 24.5 - - + -
203A GLY* 3.7 11.7 - - - +
206A MET* 3.7 31.2 - - + -
604A MET* 3.9 24.0 - - + -
606A LEU* 4.5 5.6 - - + -
635A LEU* 3.8 18.2 - - + -
687A GLU* 2.8 21.7 + - + +
688A TRP 3.8 2.7 - - - +
690A ALA* 1.3 69.0 - - - +
692A ALA* 1.3 67.1 + - - +
694A ILE* 3.3 9.4 + - + +
695A LEU* 2.9 24.9 + - + +
727A PHE* 3.6 22.0 - - + -
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A TRP* 2.7 25.7 + - + +
689A ASP* 3.4 12.6 - - - +
691A ILE* 1.3 75.0 - - - +
693A LEU* 1.3 56.9 + - - +
695A LEU* 3.2 3.1 + - - -
696A LYS 2.9 24.6 + - - -
724A TYR* 3.2 27.8 - - + -
727A PHE* 3.9 20.6 - - + -
728A THR* 4.1 7.0 - - + -
734A LEU* 5.5 4.7 - - + +
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 4.0 27.6 - - + +
164A ASP* 5.7 0.4 - - - +
167A ALA* 4.1 12.6 - - + -
685A ARG* 3.8 34.5 - - - +
689A ASP* 2.8 14.5 + - - +
690A ALA* 3.4 9.0 - - - +
692A ALA* 1.3 74.3 - - - +
694A ILE* 1.3 65.6 + - - +
696A LYS* 3.2 20.5 + - + +
697A LYS* 2.9 47.9 + - + +
724A TYR* 5.3 0.4 - - - -
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Residues in contact with ILE 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 5.9 0.2 - - + -
167A ALA* 4.3 22.2 - - + +
170A ILE* 4.0 26.7 - - + -
171A ALA* 4.2 0.2 - - - +
174A ILE* 4.0 16.8 - - + -
206A MET* 5.4 7.4 - - - -
633A PHE* 3.9 26.9 - - + -
635A LEU* 4.7 4.7 - - + -
650A LEU* 3.9 20.4 - - + -
690A ALA 3.0 20.0 + - - +
691A ILE* 3.3 16.6 + - + +
693A LEU* 1.3 74.9 - - - +
695A LEU* 1.3 63.5 + - + +
697A LYS* 3.1 4.8 + - - +
698A VAL* 2.7 31.6 + - + +
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Residues in contact with LEU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A MET* 3.9 30.1 - - + -
209A LEU* 4.7 3.8 - - + -
210A MET* 4.0 20.9 - - + -
691A ILE* 2.9 18.9 + - + +
692A ALA* 3.6 4.9 - - - +
694A ILE* 1.3 83.5 - - + +
696A LYS* 1.3 60.5 + - - +
698A VAL* 3.3 9.6 + - + +
699A GLY* 3.1 18.0 + - - -
723A LEU* 4.1 22.8 - - + +
724A TYR* 4.1 21.4 + - - +
727A PHE* 3.5 44.0 - - + -
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Residues in contact with LYS 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A ALA 2.9 10.5 + - - +
693A LEU* 3.2 24.9 + - + +
695A LEU* 1.3 70.3 - - - +
697A LYS* 1.3 57.6 + - + +
699A GLY* 3.0 4.9 + - - -
700A GLU* 2.3 75.4 + - + +
724A TYR* 3.5 44.5 - - + +
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Residues in contact with LYS 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 2.8 44.3 + - - +
167A ALA* 3.9 19.3 - - + +
168A GLY* 4.4 11.9 - - - +
171A ALA* 3.7 14.4 - - + -
693A LEU* 2.9 32.5 + - + +
694A ILE 3.4 8.3 - - - +
696A LYS* 1.3 78.6 - - - +
698A VAL* 1.3 57.5 + - - +
700A GLU* 3.2 24.4 + - + +
701A ARG* 2.7 46.5 + - + +
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Residues in contact with VAL 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA* 3.6 27.8 - - + +
174A ILE* 4.0 26.5 - - + -
175A ILE* 3.6 9.1 - - + +
694A ILE* 2.7 25.0 + - + +
695A LEU* 3.5 14.6 - - + +
696A LYS 3.3 0.2 - - - -
697A LYS* 1.3 72.2 - - - +
699A GLY* 1.3 57.5 + - - +
702A ALA* 2.9 32.9 + - - +
720A TYR* 3.8 18.4 - - + -
723A LEU* 3.7 26.7 - - + -
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Residues in contact with GLY 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A LEU 3.1 6.1 + - - -
696A LYS* 3.0 7.8 + - - -
698A VAL* 1.3 80.6 - - - +
700A GLU* 1.3 55.6 + - - +
702A ALA* 3.6 2.5 - - - +
703A ALA* 2.9 29.7 + - - +
720A TYR 3.7 24.0 + - - -
721A ASP* 4.3 11.3 - - - +
724A TYR* 6.3 0.7 - - - -
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Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A LYS* 2.3 65.3 + - + +
697A LYS* 3.2 33.8 + - + +
699A GLY* 1.3 71.0 - - - +
701A ARG* 1.3 62.4 + - + +
703A ALA* 3.1 8.1 + - - +
704A ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLY* 4.4 13.0 + - - +
171A ALA* 4.1 11.4 - - + -
172A ASP* 3.2 42.4 + - - +
175A ILE* 3.8 10.5 - - + -
697A LYS* 2.7 43.1 + - + +
700A GLU* 1.3 70.7 - - - +
702A ALA* 1.3 66.3 + - - +
704A ALA* 3.3 24.6 + - - +
705A ARG* 2.9 41.1 + - - +
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Residues in contact with ALA 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.4 11.3 - - + +
698A VAL 2.9 20.7 + - - +
699A GLY 3.6 2.5 - - - +
701A ARG* 1.3 75.7 - - - +
703A ALA* 1.3 62.7 + - - +
705A ARG* 3.1 4.3 + - - +
706A GLY 3.0 4.5 + - - -
707A LEU* 2.9 35.4 + - + +
720A TYR* 3.5 40.6 - - + -
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Residues in contact with ALA 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A GLY 2.9 15.4 + - - +
700A GLU* 3.4 10.8 - - - +
702A ALA* 1.3 77.4 - - - +
704A ALA* 1.3 57.9 + - - +
706A GLY* 3.0 19.2 + - - -
707A LEU 4.3 5.6 - - - +
721A ASP* 6.1 3.8 - - + -
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Residues in contact with ALA 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A GLU 2.9 15.5 + - - +
701A ARG* 3.3 25.1 + - - +
703A ALA* 1.3 77.1 - - - +
705A ARG* 1.3 59.0 + - - +
706A GLY 3.2 0.9 + - - -
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Residues in contact with ARG 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASP* 3.0 44.5 + - - +
175A ILE* 3.5 24.4 - - - +
176A ASP* 2.7 31.9 + - - +
179A GLU* 5.4 1.6 - - - +
701A ARG* 2.9 34.2 + - - +
702A ALA 3.6 4.3 - - - +
704A ALA* 1.3 76.9 - - - +
706A GLY* 1.3 62.2 + - - +
707A LEU* 3.3 23.7 + - + +
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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
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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) + - + + + + + -
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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