Contacts of the helix formed by residues 563 - 580 (chain A) in PDB entry 1HHS
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 ILE 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PHE* 3.7 42.4 - - + -
78A ASN* 3.8 23.1 - - + +
80A VAL* 3.5 27.6 - - + -
84A PHE* 4.3 4.5 - - + -
518A ILE* 4.1 6.7 - - + -
561A CYS* 3.1 16.8 - - - -
562A PRO* 1.3 80.2 - - - +
564A TYR* 1.3 64.5 + - - +
565A SER 3.4 2.7 - - - -
566A ASP* 3.1 14.7 + - + +
567A VAL* 2.9 39.7 + - + +
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Residues in contact with TYR 564 (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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518A ILE* 4.0 15.7 - - + -
521A MET* 4.3 3.6 - - - -
554A MET* 3.4 29.7 - - + +
555A LYS* 3.4 52.2 + - + +
558A TYR* 3.4 35.4 - - + +
559A GLY* 3.9 14.6 - - - +
561A CYS* 3.0 18.5 + - + +
562A PRO 3.4 1.2 + - - -
563A ILE* 1.3 76.9 - - - +
565A SER* 1.3 73.2 + - - +
567A VAL* 3.2 3.1 + - - +
568A LEU* 3.1 49.0 + - + +
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Residues in contact with SER 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LYS* 5.5 2.4 + - - -
562A PRO 5.2 0.6 + - - -
563A ILE 3.4 0.4 - - - -
564A TYR* 1.3 89.2 - - - +
566A ASP* 1.3 68.1 + - - +
568A LEU* 3.3 6.6 + - - +
569A GLU* 2.9 36.2 + - - +
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Residues in contact with ASP 566 (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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60A TYR* 5.6 0.5 - - - -
65A PHE* 3.5 36.1 - - + -
562A PRO 4.0 4.7 - - - +
563A ILE* 3.1 22.6 + - - +
565A SER* 1.3 80.5 + - - +
567A VAL* 1.3 58.5 + - - +
569A GLU* 3.4 7.2 + - - +
570A ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.3 23.8 - - + -
65A PHE* 5.5 0.2 - - + -
84A PHE* 5.2 1.1 - - + -
518A ILE* 3.7 25.8 - - + -
521A MET* 4.1 11.0 - - + -
522A LEU* 4.0 17.3 - - + -
563A ILE* 2.9 35.4 + - + +
564A TYR 3.7 6.7 - - - +
565A SER 3.2 0.2 - - - -
566A ASP* 1.3 75.4 - - + +
568A LEU* 1.3 66.1 + - - +
570A ALA* 3.1 6.5 + - - +
571A ILE* 2.8 40.7 + - + +
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Residues in contact with LEU 568 (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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521A MET* 4.4 6.1 - - + -
551A TRP* 4.0 18.6 - - + -
554A MET* 3.9 24.9 - - + -
564A TYR* 3.1 57.6 + - + +
565A SER* 3.8 8.7 - - - +
567A VAL* 1.3 75.7 - - - +
569A GLU* 1.3 63.5 + - + +
571A ILE* 3.3 21.5 + - + +
572A GLU* 3.0 23.2 + - - +
583A TYR* 5.5 0.7 - - + -
584A ARG* 5.8 0.6 + - - -
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Residues in contact with GLU 569 (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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565A SER* 2.9 26.9 + - - +
566A ASP* 3.8 6.9 - - - +
568A LEU* 1.3 76.1 - - + +
570A ALA* 1.3 66.3 + - - +
572A GLU* 3.3 6.8 + - + +
573A ARG* 3.0 24.6 + - - +
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Residues in contact with ALA 570 (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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57A LEU* 3.8 11.2 - - + -
60A TYR* 3.8 21.3 - - + -
61A LEU* 3.8 24.0 - - + -
566A ASP 2.9 16.9 + - - +
567A VAL 3.1 4.0 + - - +
569A GLU* 1.3 77.1 - - - +
571A ILE* 1.3 58.2 + - - +
573A ARG* 3.8 10.7 - - - +
574A CYS* 2.9 34.7 + - - +
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Residues in contact with ILE 571 (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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53A PHE* 3.7 8.8 - - + -
57A LEU* 4.1 25.1 - - + -
521A MET* 4.1 13.0 - - + -
522A LEU* 3.9 5.2 - - + -
525A GLN* 4.9 3.6 - - - +
526A PHE* 3.9 25.8 - - + -
567A VAL* 2.8 36.3 + - + +
568A LEU* 3.5 17.0 - - + +
570A ALA* 1.3 77.8 - - - +
572A GLU* 1.3 54.1 + - - +
575A TRP* 2.7 38.3 + - - +
583A TYR* 3.3 37.0 - - + -
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Residues in contact with GLU 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU 3.0 13.4 + - - +
569A GLU* 3.7 10.8 - - + +
571A ILE* 1.3 76.7 - - - +
573A ARG* 1.3 64.9 + - - +
575A TRP* 3.8 3.3 - - - +
576A TRP* 2.9 40.8 + - + +
581A GLU 4.8 0.2 - - - +
582A SER* 2.4 34.6 + - - -
583A TYR* 3.4 10.4 + - - +
584A ARG* 3.0 54.1 + - - +
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Residues in contact with ARG 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 2.9 27.9 + - - -
60A TYR* 3.1 55.6 + - - +
569A GLU 3.0 16.6 + - - +
570A ALA* 3.8 6.8 - - - +
572A GLU* 1.3 78.4 - - - +
574A CYS* 1.3 75.7 + - - +
576A TRP* 3.2 9.6 + - - +
577A ASN* 3.0 32.3 + - - +
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Residues in contact with CYS 574 (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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53A PHE* 3.6 22.5 - - + +
56A GLU* 3.5 39.6 - - + +
57A LEU* 3.8 26.2 - - + +
570A ALA 2.9 23.3 + - - +
573A ARG* 1.3 92.8 - - - +
575A TRP* 1.3 58.9 + - - +
577A ASN* 3.2 3.9 + - - +
578A ALA* 2.9 29.6 + - - +
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Residues in contact with TRP 575 (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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40A TYR* 5.6 2.5 - + - -
43A LEU* 4.5 14.8 - - + -
50A PHE* 4.0 13.2 - + - -
53A PHE* 3.6 26.2 - + + -
526A PHE* 3.9 16.2 - + - -
571A ILE 2.7 22.8 + - - +
572A GLU 3.9 1.6 - - - +
574A CYS* 1.3 71.3 - - - +
576A TRP* 1.3 58.1 + - - +
578A ALA 4.4 0.2 - - - +
579A PHE* 2.7 81.5 + + + +
580A GLY 3.6 0.3 + - - -
581A GLU* 3.5 22.9 - - - +
582A SER 4.2 1.6 - - - -
583A TYR* 3.5 48.7 - + + +
586A TYR* 3.9 33.4 - + - +
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Residues in contact with TRP 576 (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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572A GLU* 2.9 35.9 + - + +
573A ARG* 3.4 12.1 - - - +
575A TRP* 1.3 77.1 - - - +
577A ASN* 1.3 62.7 - - - +
580A GLY* 2.7 66.4 + - - +
581A GLU* 3.5 23.9 + - - -
582A SER* 3.8 17.0 - - - +
26B GLN* 4.7 15.3 - - - -
30B ARG* 5.1 10.8 - - - -
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Residues in contact with ASN 577 (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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56A GLU* 2.9 36.9 + - - +
573A ARG* 3.0 26.1 + - - +
574A CYS 3.2 7.8 + - - +
576A TRP* 1.3 83.1 - - - +
578A ALA* 1.3 60.8 + - + +
580A GLY 4.7 0.5 + - - -
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Residues in contact with ALA 578 (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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49A ARG* 3.4 46.2 - - - +
52A SER* 4.9 6.5 - - - +
53A PHE* 3.7 19.5 - - + +
574A CYS 2.9 17.4 + - - +
577A ASN* 1.3 80.4 - - - +
579A PHE* 1.3 69.3 + - + +
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Residues in contact with PHE 579 (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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43A LEU* 4.3 13.7 - - + -
49A ARG* 3.5 48.4 + - + +
50A PHE* 3.7 32.8 - + + -
53A PHE* 4.3 2.2 - - + -
575A TRP* 2.7 80.8 + + + +
578A ALA* 1.3 86.9 - - + +
580A GLY* 1.3 62.4 + - - +
581A GLU* 3.2 16.9 - - + +
33B LYS* 3.9 13.0 + - - -
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Residues in contact with GLY 580 (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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576A TRP* 2.7 48.0 + - - -
577A ASN 4.6 0.4 + - - -
578A ALA 3.7 0.4 - - - -
579A PHE* 1.3 73.5 - - - +
581A GLU* 1.3 69.9 + - - +
30B ARG* 4.7 6.9 + - - -
33B LYS* 4.3 11.0 + - - -
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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