Contacts of the strand formed by residues 552 - 561 (chain A) in PDB entry 1HKC
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 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A LYS 4.1 0.3 - - - +
546A ARG* 3.1 49.5 + - + +
550A LYS* 3.2 9.7 + - - +
551A ARG* 1.3 75.6 - - - +
553A VAL* 1.3 67.6 + - - +
554A GLU* 5.8 0.7 - - - +
667A TYR* 4.6 3.1 + - - -
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Residues in contact with VAL 553 (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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543A VAL* 3.8 19.1 - - + -
544A LYS 3.3 8.1 - - - +
545A ILE* 4.5 9.9 - - + -
551A ARG 5.6 0.2 - - - -
552A THR* 1.3 80.9 + - - +
554A GLU* 1.3 61.6 + - - +
555A MET* 3.7 27.7 - - + +
667A TYR* 3.9 28.3 - - + +
899A LYS* 4.6 16.3 - - + -
903A LEU* 6.5 0.2 - - + -
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Residues in contact with GLU 554 (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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543A VAL* 3.7 0.7 - - - +
544A LYS* 2.8 73.8 + - + +
552A THR* 5.8 1.1 - - - +
553A VAL* 1.3 74.6 - - - +
555A MET* 1.3 61.6 + - - +
556A HIS* 3.3 26.7 + - - -
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Residues in contact with MET 555 (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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541A LEU* 4.6 6.7 - - + -
542A LEU 3.1 15.5 - - - +
543A VAL* 3.9 15.9 - - + -
553A VAL* 3.7 24.2 - - + +
554A GLU* 1.3 75.6 + - - +
556A HIS* 1.3 75.3 + - - +
557A ASN* 4.4 12.0 - - - +
895A ASP* 4.0 20.0 - - - +
899A LYS* 3.5 38.6 - - + -
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Residues in contact with HIS 556 (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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541A LEU* 3.4 2.8 - - - +
542A LEU* 3.0 36.8 + - + +
544A LYS* 4.4 11.0 - - + -
554A GLU* 3.3 38.1 + - + -
555A MET* 1.3 83.0 + - - +
557A ASN* 1.3 70.7 + - - +
585A PHE* 4.2 1.8 - - - -
589A MET* 3.7 38.8 - - + -
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Residues in contact with ASN 557 (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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539A ARG* 3.9 27.0 + - - +
540A VAL 3.3 15.9 - - - +
541A LEU* 3.4 17.7 - - + +
555A MET* 4.4 9.0 - - - +
556A HIS* 1.3 82.9 - - - +
558A LYS* 1.3 61.6 + - - +
559A ILE* 5.4 6.1 - - - +
585A PHE* 4.0 6.2 - - - -
588A TYR* 5.3 4.7 + - - -
589A MET* 5.3 0.2 - - - +
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Residues in contact with LYS 558 (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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539A ARG* 3.2 17.7 - - - +
540A VAL 3.2 14.2 + - - +
557A ASN* 1.3 75.0 - - - +
559A ILE* 1.3 74.6 + - - +
560A TYR* 3.6 41.5 - - + +
584A ASP* 4.5 5.4 + - - +
585A PHE* 3.6 13.5 - - + -
588A TYR* 4.1 40.6 - - + +
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Residues in contact with ILE 559 (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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537A ASN* 4.1 25.6 - - + +
538A PHE 3.6 7.9 - - - +
539A ARG* 4.1 21.5 - - + -
557A ASN* 5.4 6.3 - - - +
558A LYS* 1.3 86.9 - - - +
560A TYR* 1.3 71.9 + - - +
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Residues in contact with TYR 560 (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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537A ASN* 3.2 4.7 - - - -
538A PHE* 2.8 57.2 + + + +
540A VAL* 3.9 28.3 - - + -
558A LYS* 3.6 47.1 - - + +
559A ILE* 1.3 80.9 - - - +
561A ALA* 1.3 60.4 + - - +
581A CYS* 3.5 34.5 - - + -
584A ASP* 2.6 32.6 + - + -
585A PHE* 3.3 19.2 + - + +
588A TYR* 4.9 0.2 - - - +
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Residues in contact with ALA 561 (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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536A THR* 3.1 10.3 - - + +
537A ASN* 3.7 14.1 - - - +
538A PHE* 4.1 0.5 - - - -
560A TYR* 1.3 75.6 - - - +
562A ILE* 1.3 63.6 + - - +
563A PRO* 3.8 4.1 - - + +
577A HIS* 2.9 23.4 + - - -
581A CYS* 4.8 0.2 - - - -
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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