Contacts of the helix formed by residues 708 - 723 (chain A) in PDB entry 1Y8B
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 THR 708 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A LEU* 3.7 20.5 + - - +
639A SER* 3.8 15.9 - - - +
640A GLN* 3.3 44.4 + - + +
643A ALA* 5.1 5.2 - - + -
696A LEU* 5.4 3.7 - - - +
700A GLY* 3.7 22.2 - - - +
703A GLN* 2.7 24.2 + - - +
707A TYR* 1.3 71.8 - - - +
709A GLU* 1.3 66.6 + - - +
710A PRO* 3.4 1.1 - - - -
711A LEU* 3.6 13.1 + - - +
712A LEU 3.7 4.7 + - - -
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Residues in contact with GLU 709 (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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271A CYS* 3.3 11.5 - - - +
274A SER 5.2 0.2 - - - +
275A VAL 4.7 0.7 - - - -
276A ALA* 3.0 24.0 + - + +
632A ARG* 3.5 17.4 + - - +
635A LEU* 4.1 27.7 + - + +
636A ARG* 3.2 32.2 - - - +
707A TYR* 5.0 3.6 - - + -
708A THR* 1.3 83.1 + - - +
710A PRO* 1.3 63.9 - - + +
711A LEU 3.4 0.5 + - - -
712A LEU* 3.4 3.5 + - - +
713A HIS* 2.6 41.5 + - + +
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Residues in contact with PRO 710 (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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277A ALA* 4.8 14.4 - - + +
342A HIS* 5.1 12.6 - - + -
704A PRO* 4.5 20.4 - - + -
705A ASN* 5.6 2.7 - - - +
707A TYR* 3.4 36.1 - - + +
708A THR 3.4 3.4 - - - -
709A GLU* 1.3 96.5 - - + +
711A LEU* 1.3 66.5 + - - +
713A HIS* 3.2 12.0 + - + +
714A ALA* 2.8 21.7 + - - +
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Residues in contact with LEU 711 (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 LEU* 4.0 18.2 - - + -
699A LEU* 3.7 48.2 - - + +
700A GLY* 5.3 2.2 - - - -
702A LYS 5.1 0.4 - - - +
703A GLN* 4.1 6.5 - - + -
704A PRO* 3.8 24.8 - - + +
707A TYR 4.8 0.8 + - - -
708A THR* 3.6 13.8 + - - +
709A GLU 3.3 0.6 - - - -
710A PRO* 1.3 78.9 - - - +
712A LEU* 1.3 56.5 + - - +
714A ALA* 2.6 37.3 + - + +
715A TRP* 3.2 29.2 + - + +
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Residues in contact with LEU 712 (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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606A TYR* 4.2 11.7 - - + -
607A VAL* 3.7 22.9 - - + -
610A TRP* 5.5 1.8 - - + -
611A VAL* 4.5 9.4 - - + -
635A LEU* 3.5 35.2 - - + -
696A LEU* 3.8 25.2 - - + +
708A THR 3.7 2.0 + - - -
709A GLU 3.4 9.3 + - - +
710A PRO 3.4 0.4 - - - -
711A LEU* 1.3 80.4 - - - +
713A HIS* 1.3 74.3 + - + +
714A ALA 3.0 0.3 + - - -
715A TRP* 3.0 14.4 + - + +
716A ARG* 3.2 35.9 + - + +
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Residues in contact with HIS 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 2.9 32.3 - - + +
277A ALA* 3.2 31.4 - - + +
278A VAL* 5.5 1.3 - - + -
606A TYR* 5.2 4.3 - + - -
610A TRP* 5.6 2.7 - + - -
632A ARG* 3.5 23.3 + - - -
635A LEU* 6.2 0.4 - - + -
709A GLU* 2.6 35.4 + - + +
710A PRO* 3.2 5.6 + - + +
711A LEU 3.2 0.6 - - - -
712A LEU* 1.3 85.6 - - + +
714A ALA* 1.3 62.1 + - - +
716A ARG* 2.8 37.4 + - - +
717A LEU* 3.1 29.7 + - + +
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Residues in contact with ALA 714 (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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704A PRO* 6.0 3.1 - - + -
710A PRO 2.8 12.4 + - - +
711A LEU* 2.6 32.7 + - + +
713A HIS* 1.3 72.4 - - - +
715A TRP* 1.3 67.2 + - + +
717A LEU* 4.2 4.1 - - - +
718A ARG* 3.9 21.5 + - - +
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Residues in contact with TRP 715 (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 CYS* 4.7 16.4 - - + -
691A LYS* 5.0 7.6 - - + -
692A ALA* 3.3 35.0 - - + -
695A ASP* 2.9 34.1 - - + +
696A LEU* 5.3 3.4 - - + -
699A LEU* 4.2 17.8 - - + +
711A LEU* 3.6 31.6 - - + +
712A LEU* 3.0 9.8 + - + +
714A ALA* 1.3 79.9 - - + +
716A ARG* 1.3 69.1 + - + +
717A LEU 3.2 1.3 - - - -
718A ARG* 2.7 24.2 + - - +
719A GLU* 2.9 10.3 + - - +
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Residues in contact with ARG 716 (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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278A VAL* 3.6 16.2 - - - +
282A ASP* 2.7 30.2 + - - +
610A TRP* 3.2 45.4 - - - +
611A VAL* 4.0 17.5 - - + +
712A LEU* 3.2 27.5 + - + +
713A HIS* 2.8 45.0 + - - +
715A TRP* 1.3 78.8 - - + +
717A LEU* 1.3 56.8 + - - +
719A GLU* 2.4 38.7 + - + +
720A LYS* 2.8 13.8 + - - +
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Residues in contact with LEU 717 (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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277A ALA* 4.6 0.9 - - + +
278A VAL* 4.5 8.5 - - - -
279A ASP* 3.1 48.9 - - + +
281A GLU* 3.8 23.8 - - + +
282A ASP* 3.6 20.6 - - - +
713A HIS* 3.1 24.7 + - + +
714A ALA* 4.2 6.1 - - - +
716A ARG* 1.3 85.5 - - - +
718A ARG* 1.3 63.4 + - + +
720A LYS* 3.5 5.0 + - - +
721A GLU* 3.4 32.3 + - - +
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Residues in contact with ARG 718 (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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714A ALA 3.9 16.2 + - - +
715A TRP* 2.7 21.9 + - - +
717A LEU* 1.3 75.9 - - + +
719A GLU* 1.3 48.8 + - - -
721A GLU* 4.5 9.7 - - - +
722A SER* 2.4 37.9 + - - -
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Residues in contact with GLU 719 (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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611A VAL* 3.0 45.9 - - - +
688A CYS* 5.7 3.1 - - + +
689A ALA* 4.8 8.4 + - - +
715A TRP 2.9 5.8 + - - +
716A ARG* 2.4 35.1 + - - +
718A ARG* 1.3 72.7 - - - +
720A LYS* 1.3 62.1 + - - +
722A SER* 3.5 16.9 - - - -
723A HIS* 3.8 6.4 + - - +
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Residues in contact with LYS 720 (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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281A GLU* 4.4 22.9 - - + +
282A ASP* 3.8 30.1 - - - +
284A ILE* 5.8 4.3 - - - -
716A ARG 2.8 11.5 + - - +
717A LEU 3.9 4.9 - - - +
719A GLU* 1.3 78.5 - - - +
721A GLU* 1.3 63.3 + - - +
723A HIS 3.0 25.4 + - - +
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Residues in contact with GLU 721 (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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281A GLU* 3.2 39.5 - - + +
717A LEU* 3.4 18.7 + - - +
718A ARG* 4.5 8.9 - - - +
720A LYS* 1.3 74.1 - - - +
722A SER* 1.3 67.0 + - - +
723A HIS* 3.2 1.4 + - - -
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Residues in contact with SER 722 (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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718A ARG 2.4 28.1 + - - -
719A GLU* 3.5 12.5 - - - -
720A LYS 3.1 0.6 - - - -
721A GLU* 1.3 78.9 - - - +
723A HIS* 1.3 65.8 + - - +
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Residues in contact with HIS 723 (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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719A GLU 3.8 6.7 + - - +
720A LYS* 3.0 20.9 + - - +
721A GLU 3.2 2.4 - - - -
722A SER* 1.3 85.9 + - - +
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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
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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