Contacts of the helix formed by residues 611 - 624 (chain B) in PDB entry 1HWL
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 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B ALA* 3.4 15.5 - - + +
608B TRP* 2.7 26.1 + - + +
610B GLU* 1.3 80.8 - - - +
612B SER* 1.3 65.7 + - - +
613B GLU* 3.4 20.3 - - + +
614B GLY* 3.0 14.4 + - - -
615B PHE* 3.1 20.5 + - - +
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Residues in contact with SER 612 (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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610B GLU 3.8 1.8 + - - -
611B THR* 1.3 72.3 - - - +
613B GLU* 1.3 77.9 + - - +
615B PHE* 3.7 7.4 + - - +
616B ALA* 3.2 23.6 + - - +
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Residues in contact with GLU 613 (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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611B THR* 3.4 23.1 - - + +
612B SER* 1.3 90.4 + - - +
614B GLY* 1.3 66.0 + - - +
616B ALA* 3.4 5.7 + - - +
617B VAL* 3.0 30.5 + - + +
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Residues in contact with GLY 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B TRP* 3.4 43.5 - - - +
609B LEU* 4.7 0.9 - - - -
611B THR* 3.0 18.8 + - - -
613B GLU* 1.3 77.5 - - - +
615B PHE* 1.3 62.1 + - - +
617B VAL 3.4 0.2 + - - -
618B ILE* 3.2 26.9 + - - +
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Residues in contact with PHE 615 (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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609B LEU* 3.9 12.6 + - - +
610B GLU 5.7 0.4 - - - -
611B THR 3.1 15.5 + - - +
612B SER* 4.0 7.2 - - - +
614B GLY* 1.3 74.5 - - - +
616B ALA* 1.3 59.8 + - - +
618B ILE* 3.0 6.6 + - + +
619B LYS* 2.7 59.8 + - + +
631B LEU* 3.7 26.7 - - + -
632B GLN* 3.3 31.2 - - - -
633B LYS* 4.6 2.0 - - - -
634B LEU* 4.1 29.8 - - + -
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Residues in contact with ALA 616 (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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612B SER 3.2 16.6 + - - +
613B GLU* 3.7 6.7 - - - +
615B PHE* 1.3 82.3 - - + +
617B VAL* 1.3 57.0 + - + +
619B LYS* 3.4 9.0 + - - +
620B GLU* 2.9 32.4 + - - +
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Residues in contact with VAL 617 (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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608B TRP* 4.2 6.1 - - + -
613B GLU* 3.0 18.4 + - + +
614B GLY* 3.5 9.0 - - - +
615B PHE 3.1 0.2 - - - -
616B ALA* 1.3 77.3 - - + +
618B ILE* 1.3 61.3 - - - +
620B GLU* 3.3 9.6 + - - +
621B ALA* 3.2 21.0 + - - +
670B LYS* 3.7 17.3 - - + +
674B TYR* 3.6 42.8 - - + +
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Residues in contact with ILE 618 (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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608B TRP* 3.7 19.5 - - + -
609B LEU* 3.8 12.8 - - + -
614B GLY 3.2 13.9 + - - +
615B PHE* 3.0 9.0 + - + +
617B VAL* 1.3 72.5 - - - +
619B LYS* 1.3 62.0 + - - +
621B ALA* 3.2 6.2 + - - +
622B PHE* 2.9 26.3 + - - +
631B LEU* 4.1 9.2 - - + -
634B LEU* 4.7 8.1 - - + -
647B PHE* 3.9 18.2 - - + -
667B ALA* 3.7 36.7 - - + +
670B LYS* 4.4 7.6 - - + -
671B LEU* 4.0 23.6 - - + +
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Residues in contact with LYS 619 (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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615B PHE* 2.7 42.0 + - + +
616B ALA* 3.7 7.6 - - - +
618B ILE* 1.3 74.0 - - - +
620B GLU* 1.3 57.6 + - - +
622B PHE* 4.3 0.2 - - - -
623B ASP* 2.7 66.9 + - - +
630B ARG* 3.8 7.7 - - - +
631B LEU* 3.0 45.3 + - + +
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Residues in contact with GLU 620 (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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616B ALA 2.9 18.2 + - - +
617B VAL* 3.5 7.7 - - - +
618B ILE 3.2 0.4 - - - -
619B LYS* 1.3 77.4 - - - +
621B ALA* 1.3 62.1 + - - +
623B ASP* 3.8 4.1 - - - +
624B SER* 3.0 28.6 + - - -
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Residues in contact with ALA 621 (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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617B VAL 3.2 6.5 + - - +
618B ILE 3.2 8.4 + - - +
620B GLU* 1.3 78.8 - - - +
622B PHE* 1.3 61.8 + - - +
624B SER* 2.8 22.4 + - - -
625B THR* 3.7 0.7 - - - +
666B LYS* 3.5 27.4 - - + +
667B ALA* 4.2 9.4 - - - -
670B LYS* 3.7 36.6 - - + -
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Residues in contact with PHE 622 (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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618B ILE 2.9 16.6 + - - +
619B LYS 3.7 2.9 - - - +
621B ALA* 1.3 77.4 - - - +
623B ASP* 1.3 72.2 + - - +
624B SER 3.1 0.7 + - - -
625B THR* 2.9 27.0 + - - -
629B ALA* 3.5 18.8 - - + +
631B LEU* 3.6 20.0 - - + -
647B PHE* 3.8 25.4 - + + -
649B SER* 3.6 32.5 - - - -
659B MET 5.2 0.4 - - - -
660B ILE* 3.8 24.5 - - + -
663B GLY* 3.3 41.1 - - - +
664B THR* 3.5 11.4 - - - -
667B ALA* 4.2 4.4 - - + +
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Residues in contact with ASP 623 (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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619B LYS* 2.7 51.9 + - - +
620B GLU* 4.0 3.8 - - - +
622B PHE* 1.3 76.7 - - - +
624B SER* 1.3 56.9 + - - +
625B THR 3.2 0.9 - - - -
626B SER 3.1 9.8 - - - +
629B ALA* 2.8 24.5 - - - +
630B ARG* 2.9 39.9 + - - +
631B LEU* 2.9 18.7 + - - +
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Residues in contact with SER 624 (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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620B GLU* 3.0 18.0 + - - -
621B ALA* 2.8 14.6 + - - -
622B PHE 3.1 0.4 - - - -
623B ASP* 1.3 75.6 - - - +
625B THR* 1.3 59.1 + - - +
626B SER 3.5 0.7 - - - -
666B LYS* 2.7 37.6 + - - -
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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