Contacts of the helix formed by residues 561 - 575 (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 CYS 561 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A FBI 3.6 31.1 - - + +
528A GLU* 2.8 29.1 + - - -
559B GLU 3.5 0.2 + - - -
560B GLY* 1.3 74.1 - - - +
562B LEU* 1.3 54.0 + - - +
564B ALA* 3.7 6.2 - - + +
565B SER* 2.7 36.6 + - - -
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Residues in contact with LEU 562 (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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2A FBI 3.5 14.6 - - + +
555B MET* 3.9 13.5 - - + -
557B THR* 3.8 26.7 - - + +
559B GLU* 3.4 26.8 + - + +
560B GLY 3.2 4.4 + - - -
561B CYS* 1.3 77.7 - - - +
563B VAL* 1.3 63.7 + - - +
565B SER* 3.8 0.7 - - - -
566B THR* 2.9 38.7 + - - +
752B HIS* 3.9 18.8 - - + -
755B ASN* 3.8 44.9 - - + +
756B ILE* 4.0 4.3 - - + -
759B ALA* 4.5 0.4 - - + -
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Residues in contact with VAL 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A CYS* 4.0 15.9 - - - -
528A GLU* 3.4 31.4 + - + +
529A ASN* 4.2 3.4 - - + +
539B GLY* 4.2 2.2 - - - -
540B VAL 3.6 31.4 - - - +
541B ALA* 4.3 3.4 - - + +
555B MET* 4.1 27.1 - - + -
557B THR* 3.9 24.9 - - + -
559B GLU 4.8 0.6 + - - -
562B LEU* 1.3 74.5 - - - +
564B ALA* 1.3 58.7 + - - +
566B THR* 3.2 2.8 + - - -
567B ASN* 2.9 27.7 + - - +
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Residues in contact with ALA 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A FBI 5.9 0.9 - - + -
101A ADP 3.5 53.9 - - + +
528A GLU* 3.0 21.6 + - + +
561B CYS* 3.7 10.1 - - + +
562B LEU 3.3 0.2 - - - -
563B VAL* 1.3 77.0 - - - +
565B SER* 1.3 61.2 + - - +
567B ASN* 3.3 3.5 + - - +
568B ARG* 3.0 18.9 + - - +
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Residues in contact with SER 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A FBI 2.7 45.4 + - - +
561B CYS 2.7 22.6 + - - -
562B LEU* 3.8 3.4 - - - -
564B ALA* 1.3 73.4 - - - +
566B THR* 1.3 62.6 + - - +
568B ARG* 3.2 4.8 + - - +
569B GLY 3.1 6.2 + - - -
752B HIS* 5.4 1.8 - - - -
849B GLY* 5.0 1.3 + - - -
852B SER* 2.8 46.6 + - - -
853B LEU* 4.0 4.5 + - - +
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Residues in contact with THR 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ALA* 4.0 5.8 - - + -
555B MET* 3.5 25.7 - - + +
562B LEU* 2.9 25.6 + - - +
563B VAL 3.7 3.6 - - - -
565B SER* 1.3 72.6 - - - +
567B ASN* 1.3 61.7 + - - +
569B GLY* 3.1 2.6 + - - +
570B CYS* 2.9 28.1 + - - -
752B HIS* 5.3 0.3 - - - -
756B ILE* 4.0 7.7 - - + +
845B THR* 3.7 39.7 - - + +
848B ALA* 3.9 3.5 - - + +
849B GLY* 4.3 13.6 - - - +
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Residues in contact with ASN 567 (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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101A ADP 3.2 45.7 + - + +
479A TYR* 4.5 6.3 - - - -
529A ASN* 4.0 8.7 - - - +
540B VAL 4.1 1.0 - - - +
541B ALA* 3.4 11.4 - - - +
542B GLY 2.7 41.8 + - - +
563B VAL 2.9 16.9 + - - +
564B ALA 3.5 5.8 - - - +
566B THR* 1.3 72.8 - - - +
568B ARG* 1.3 66.1 + - - +
570B CYS* 3.1 6.6 + - - +
571B ARG* 3.0 19.6 + - - +
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Residues in contact with ARG 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A FBI 4.0 10.3 + - - -
101A ADP 3.2 34.0 + - - +
564B ALA 3.0 12.7 + - - +
565B SER* 3.2 9.5 + - - +
567B ASN* 1.3 76.6 - - - +
569B GLY* 1.3 62.7 + - - +
571B ARG* 3.2 6.0 + - - +
572B ALA* 3.1 21.0 + - - +
720B VAL* 3.5 37.9 + - + +
721B LEU* 3.9 21.8 + - + +
722B LYS* 4.3 10.5 - - - +
852B SER* 3.0 41.3 + - - +
855B ALA* 4.0 3.8 - - - +
856B ALA* 3.8 20.8 - - - +
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Residues in contact with GLY 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B SER 3.1 7.7 + - - -
566B THR 3.1 4.7 + - - -
568B ARG* 1.3 77.8 - - - +
570B CYS* 1.3 61.3 + - - +
572B ALA* 3.3 7.5 + - - +
573B ILE* 3.1 26.0 + - - +
721B LEU* 5.1 1.1 - - - -
848B ALA* 3.3 31.6 - - - -
851B LEU* 4.0 4.7 - - - +
852B SER* 3.9 9.2 - - - -
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Residues in contact with CYS 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ALA* 4.4 7.0 - - - -
542B GLY* 4.3 20.0 - - - -
543B PRO 3.6 21.0 - - - +
544B LEU* 3.9 25.8 - - - -
545B CYS 5.3 1.2 + - - -
553B VAL* 5.7 0.7 - - - -
566B THR* 2.9 22.2 + - - -
567B ASN* 3.4 9.4 - - - +
569B GLY* 1.3 76.8 - - - +
571B ARG* 1.3 56.7 + - - +
573B ILE* 3.2 7.5 + - - +
574B GLY* 2.9 26.5 + - - -
845B THR* 5.3 3.4 - - - -
848B ALA* 3.6 16.3 - - - +
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Residues in contact with ARG 571 (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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101A ADP 4.3 20.0 + - - +
543B PRO 5.6 0.2 - - - -
567B ASN 3.0 12.0 + - - +
568B ARG* 3.3 14.1 - - - +
570B CYS* 1.3 76.3 - - - +
572B ALA* 1.3 62.5 + - - +
574B GLY* 3.2 2.8 + - - -
575B LEU* 3.0 66.0 + - + +
720B VAL* 4.2 15.6 - - + +
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Residues in contact with ALA 572 (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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568B ARG 3.1 9.0 + - - +
569B GLY 3.6 8.7 - - - +
571B ARG* 1.3 78.4 - - - +
573B ILE* 1.3 62.3 + - - +
575B LEU* 3.5 0.7 + - - -
576B GLY* 3.2 17.8 + - - -
712B ILE* 3.9 8.1 - - + +
716B VAL* 3.8 29.7 - - + +
720B VAL* 4.2 4.7 - - + -
721B LEU* 4.1 22.7 - - + -
851B LEU* 4.1 14.8 - - + -
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Residues in contact with ILE 573 (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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544B LEU* 4.4 13.5 - - + -
545B CYS* 4.0 7.6 - - + +
569B GLY 3.1 9.6 + - - +
570B CYS* 3.5 7.4 - - - +
571B ARG 3.2 0.2 - - - -
572B ALA* 1.3 77.9 - - - +
574B GLY* 1.3 58.4 + - - +
576B GLY* 3.0 12.3 + - - -
577B GLY 3.4 0.2 + - - -
578B GLY* 2.9 26.5 + - - +
579B ALA* 3.8 30.3 - - + +
710B ALA* 4.5 6.1 - - + -
712B ILE* 4.1 10.9 - - + +
844B GLY 4.5 0.4 - - - +
847B MET* 3.9 22.0 - - + -
848B ALA* 3.8 35.4 - - + +
851B LEU* 3.8 16.2 - - + -
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Residues in contact with GLY 574 (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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545B CYS* 3.8 30.7 - - - -
570B CYS 2.9 13.4 + - - -
571B ARG* 3.2 3.8 + - - -
573B ILE* 1.3 75.3 - - - +
575B LEU* 1.3 61.4 + - - +
576B GLY 3.0 0.2 - - - -
577B GLY* 3.2 14.2 + - - -
578B GLY 4.0 0.3 + - - -
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Residues in contact with LEU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B ARG* 3.0 55.8 + - - +
572B ALA 3.8 2.9 - - - +
574B GLY* 1.3 76.3 - - - +
576B GLY* 1.3 58.8 + - - +
577B GLY 3.3 0.6 + - - -
713B PRO* 4.2 5.2 - - - +
716B VAL* 3.8 27.3 - - + +
720B VAL* 3.7 29.2 - - + -
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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