Contacts of the helix formed by residues 708 - 720 (chain A) in PDB entry 3H44
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
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Residue Dist Surf HB Arom Phob DC
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659A PHE* 3.7 6.1 - - - -
705A ASP 4.6 4.3 - - - +
706A ASP 3.4 9.7 + - - +
707A VAL* 1.3 78.5 - - - +
709A LEU* 1.3 64.2 + - - +
710A PRO* 3.6 13.3 - - - +
711A ARG* 2.8 46.5 + - - +
712A LEU* 3.1 23.0 + - - +
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Residues in contact with LEU 709 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A ILE* 3.7 42.0 - - + +
656A GLU* 3.4 54.1 - - + +
659A PHE* 3.6 28.4 - - + -
708A THR* 1.3 71.7 - - - +
710A PRO* 1.4 74.6 - - + +
712A LEU* 3.2 1.4 + - + -
713A LYS* 3.1 36.4 + - + +
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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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708A THR* 3.6 11.9 - - - +
709A LEU* 1.4 95.5 - - + +
711A ARG* 1.3 66.6 + - - +
712A LEU 3.2 0.9 + - - -
713A LYS* 3.4 8.8 + - + +
714A ALA* 3.3 20.5 + - - +
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Residues in contact with ARG 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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588A LEU* 5.2 11.8 - - + +
592A MET* 3.9 16.4 - - - +
706A ASP* 3.2 35.1 + - - +
708A THR* 2.8 42.7 + - - +
710A PRO* 1.3 84.3 - - - +
712A LEU* 1.3 56.4 + - - +
714A ALA* 3.6 6.2 - - - +
715A PHE* 3.1 23.9 + - - +
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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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592A MET* 3.8 29.6 - - + +
595A LEU* 4.5 3.1 - - + -
596A TYR* 4.3 12.8 - - + +
599A LEU* 3.8 29.6 - - + -
654A ILE* 3.8 17.0 - - + -
659A PHE* 4.2 17.9 - - + -
707A VAL* 4.9 3.4 - - + -
708A THR 3.1 14.8 + - - +
709A LEU* 3.8 3.6 - - - +
711A ARG* 1.3 74.1 - - - +
713A LYS* 1.3 66.9 + - - +
714A ALA 3.0 1.1 - - - -
715A PHE* 2.9 37.1 + - + -
716A ILE* 3.1 18.0 + - + +
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Residues in contact with LYS 713 (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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652A PHE 3.7 16.2 + - - -
653A GLU* 3.9 7.7 - - - +
654A ILE* 3.4 48.4 + - + +
709A LEU* 3.1 33.3 + - + +
710A PRO* 3.7 8.7 - - + +
712A LEU* 1.3 74.3 - - - +
714A ALA* 1.3 57.8 + - - +
716A ILE* 4.2 4.9 - - - +
717A PRO* 2.9 27.4 - - - +
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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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710A PRO 3.3 9.6 + - - +
711A ARG* 3.6 11.4 - - - +
712A LEU 3.0 0.6 - - - -
713A LYS* 1.3 77.6 - - - +
715A PHE* 1.3 67.2 + - - +
717A PRO* 3.1 13.0 - - - +
718A GLN* 3.5 14.9 + - + +
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Residues in contact with PHE 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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582A PHE* 3.6 13.5 - - + -
589A HIS* 3.3 42.0 - + - -
592A MET* 3.5 30.5 - - + -
593A ALA* 3.3 41.1 - - + -
596A TYR* 4.5 3.4 - - + -
711A ARG 3.1 14.8 + - - +
712A LEU* 2.9 17.1 + - + +
714A ALA* 1.3 75.1 - - - +
716A ILE* 1.3 69.9 + - + +
718A GLN* 3.0 12.7 - - + +
719A LEU* 3.0 54.2 + - + +
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Residues in contact with ILE 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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596A TYR* 3.4 51.6 - - + +
649A MET 4.3 4.3 - - - +
650A ALA 5.9 0.7 - - - +
652A PHE* 4.0 18.8 - - + +
654A ILE* 3.8 29.2 - - + -
712A LEU* 3.1 15.6 + - + +
713A LYS* 4.2 4.3 - - - +
715A PHE* 1.3 83.1 - - + +
717A PRO* 1.4 69.8 - - + +
719A LEU* 3.3 3.7 + - - +
720A LEU* 3.0 48.7 + - + +
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Residues in contact with PRO 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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713A LYS 2.9 28.7 - - - +
714A ALA* 3.1 12.3 - - - +
716A ILE* 1.4 85.6 - - + +
718A GLN* 1.3 67.4 + - - +
720A LEU* 3.4 7.9 + - + +
721A SER* 3.2 23.4 + - - -
753A ALA* 5.1 4.8 - - + +
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Residues in contact with GLN 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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582A PHE* 3.1 49.5 - - + -
589A HIS* 5.7 3.4 - - + -
714A ALA 3.5 12.9 + - - +
715A PHE* 3.0 16.4 - - + +
717A PRO* 1.3 77.8 - - - +
719A LEU* 1.3 61.1 + - - +
721A SER* 2.7 28.2 + - - -
722A ARG* 4.2 1.2 + - - +
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Residues in contact with LEU 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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580A SER* 3.5 36.1 + - - +
582A PHE* 4.0 8.3 - - + +
583A ALA* 3.8 25.1 - - + +
593A ALA* 5.2 3.6 - - + -
596A TYR* 4.1 25.1 - - + -
626A GLY* 5.6 0.2 - - - -
627A MET* 4.2 23.8 - - + -
715A PHE* 3.0 39.1 + - + +
716A ILE 3.5 6.7 - - - +
718A GLN* 1.3 80.0 - - - +
720A LEU* 1.3 58.7 + - + +
721A SER 3.3 3.5 + - - -
722A ARG 3.6 4.5 + - - +
723A LEU* 3.3 20.6 - - - +
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Residues in contact with LEU 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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596A TYR* 3.6 11.7 - - + +
627A MET* 4.5 17.7 - - + -
649A MET* 3.5 30.5 - - + +
650A ALA* 4.1 13.2 - - - +
716A ILE* 3.0 35.6 + - + +
717A PRO* 3.7 7.0 - - + +
718A GLN 3.3 0.2 - - - -
719A LEU* 1.3 78.0 - - + +
721A SER* 1.3 53.2 + - - +
722A ARG 3.6 0.9 - - - -
723A LEU* 4.0 12.9 - - + +
749A LEU* 4.3 19.3 - - + -
753A ALA* 3.9 16.1 - - + +
755A THR* 2.7 33.9 + - - +
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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