Contacts of the helix formed by residues 708 - 721 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659B PHE* 3.7 6.7 - - - -
705B ASP 4.6 5.4 - - - +
706B ASP* 3.1 15.2 + - - +
707B VAL* 1.3 76.7 - - - +
709B LEU* 1.3 66.6 + - - +
710B PRO* 3.5 16.3 - - - +
711B ARG* 3.0 36.6 + - - +
712B LEU* 3.1 13.7 + - - +
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Residues in contact with LEU 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B ILE* 3.7 35.2 - - + +
656B GLU* 3.1 37.5 - - + +
659B PHE* 3.6 28.9 - - + -
660B GLU* 5.7 0.7 - - - +
708B THR* 1.3 72.5 - - - +
710B PRO* 1.4 72.9 - - + +
712B LEU* 3.0 14.8 + - + +
713B LYS* 3.1 39.8 + - + +
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Residues in contact with PRO 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B THR* 3.5 18.6 - - - +
709B LEU* 1.4 97.2 - - + +
711B ARG* 1.3 62.2 + - + +
712B LEU 3.1 0.3 + - - -
713B LYS* 3.3 11.2 + - + +
714B ALA* 3.1 23.6 + - - +
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Residues in contact with ARG 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B LEU* 3.4 31.0 - - - +
589B HIS* 5.3 2.4 + - - -
592B MET* 3.6 15.9 - - - +
706B ASP* 3.3 29.4 + - - +
707B VAL* 4.9 0.7 - - - +
708B THR* 3.0 25.9 + - - +
710B PRO* 1.3 77.2 - - + +
712B LEU* 1.3 55.8 + - - +
714B ALA* 3.7 7.6 - - - +
715B PHE* 3.1 24.8 + - - +
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Residues in contact with LEU 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B MET* 3.8 30.0 - - + +
595B LEU* 4.8 7.0 - - + -
596B TYR* 4.3 10.5 - - + +
599B LEU* 3.8 25.8 - - + -
654B ILE* 3.8 21.1 - - + -
659B PHE* 3.8 21.5 - - + -
707B VAL* 4.7 2.5 - - + -
708B THR 3.1 9.4 + - - +
709B LEU* 3.0 10.3 + - - +
711B ARG* 1.3 73.9 - - - +
713B LYS* 1.3 60.1 + - - +
714B ALA 3.2 1.1 - - - -
715B PHE* 2.9 40.3 + - + +
716B ILE* 3.2 23.7 + - + +
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Residues in contact with LYS 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B GLU* 6.1 2.0 - - - +
654B ILE* 3.9 34.4 + - + +
709B LEU* 3.1 43.6 + - + +
710B PRO* 3.6 9.9 - - + +
712B LEU* 1.3 75.1 - - - +
714B ALA* 1.3 58.3 - - - +
716B ILE* 3.7 3.8 + - - +
717B PRO* 2.9 29.3 - - - +
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Residues in contact with ALA 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B PRO 3.1 16.3 + - - +
711B ARG* 3.7 8.5 - - - +
713B LYS* 1.3 77.8 - - - +
715B PHE* 1.3 62.6 + - - +
717B PRO* 3.4 8.6 - - - +
718B GLN* 3.2 20.1 + - + +
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Residues in contact with PHE 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B PHE* 3.3 31.0 - - + -
589B HIS* 3.9 17.9 - + + -
592B MET* 3.6 35.7 - - + -
593B ALA* 3.4 37.7 - - + -
596B TYR* 4.4 5.2 - - + -
711B ARG 3.1 15.8 + - - +
712B LEU* 2.9 19.1 + - + +
714B ALA* 1.3 77.5 - - - +
716B ILE* 1.3 56.2 + - + +
718B GLN* 3.1 8.6 - - + +
719B LEU* 2.6 65.9 + - + +
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Residues in contact with ILE 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596B TYR* 3.6 59.5 - - + +
649B MET 4.5 3.4 - - - +
650B ALA 6.3 0.4 - - - -
652B PHE* 4.7 12.6 - - + +
654B ILE* 3.7 28.3 - - + -
712B LEU* 3.2 19.7 + - + +
713B LYS* 4.6 3.1 - - - -
715B PHE* 1.3 78.6 - - + +
717B PRO* 1.3 69.8 - - + +
718B GLN 3.0 1.1 - - - -
719B LEU* 2.9 7.3 + - - +
720B LEU* 2.7 39.2 + - + +
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Residues in contact with PRO 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B LYS 2.9 29.2 - - - +
714B ALA* 3.4 6.1 - - - +
716B ILE* 1.3 85.3 - - + +
718B GLN* 1.3 58.0 - - - +
720B LEU* 4.2 6.9 - - + +
721B SER* 2.9 33.1 + - - -
753B ALA* 5.0 6.8 - - + +
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Residues in contact with GLN 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B PHE* 3.4 50.7 - - - -
589B HIS* 4.6 11.9 - - - -
714B ALA* 3.2 15.2 + - + +
715B PHE* 3.1 14.7 - - + +
717B PRO* 1.3 82.7 - - - +
719B LEU* 1.3 60.8 + - - +
721B SER* 3.5 17.2 + - - -
722B ARG 4.6 0.7 + - - -
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Residues in contact with LEU 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B SER* 3.4 36.1 + - - +
582B PHE* 4.3 6.5 - - + -
583B ALA* 4.2 16.6 - - + +
593B ALA* 5.4 3.6 - - + -
596B TYR* 3.9 26.7 - - + -
626B GLY* 5.9 0.9 - - - -
627B MET* 4.1 19.7 - - + -
715B PHE* 2.6 53.2 + - + +
716B ILE* 3.3 4.3 - - - +
718B GLN* 1.3 75.7 - - - +
720B LEU* 1.3 67.4 + - + +
721B SER 3.5 0.3 + - - -
722B ARG 3.9 3.6 - - - +
723B LEU* 3.5 15.0 - - + +
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Residues in contact with LEU 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B TYR* 3.7 23.6 - - - +
627B MET* 4.4 18.8 - - + -
649B MET* 3.8 8.1 - - + +
650B ALA* 3.7 28.7 - - + +
716B ILE* 2.7 30.6 + - + +
717B PRO* 4.2 5.2 - - + +
719B LEU* 1.3 81.8 - - + +
721B SER* 1.3 61.7 + - - +
722B ARG 3.0 1.9 + - - -
723B LEU* 3.4 27.4 - - + +
749B LEU* 4.6 8.5 - - + -
753B ALA* 4.0 18.6 - - + -
755B THR* 2.7 22.8 + - - -
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Residues in contact with SER 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B PRO 2.9 18.7 + - - -
718B GLN* 3.5 12.6 + - - -
719B LEU 3.3 1.4 - - - -
720B LEU* 1.3 76.3 - - - +
722B ARG* 1.3 70.7 + - - +
753B ALA 4.3 12.8 + - - -
754B HIS 4.6 2.0 - - - -
755B THR* 3.4 1.8 - - - +
756B LYS* 3.1 41.5 + - - +
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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