Contacts of the strand formed by residues 555 - 560 (chain A) in PDB entry 1YC0
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 ARG 555 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ILE* 3.7 22.0 + - + +
411A GLY* 2.7 43.6 + - - +
412A SER* 2.9 13.6 - - - +
413A SER* 3.6 22.2 - - - +
414A SER* 4.6 0.7 - - - -
538A ALA* 3.0 8.3 - - - +
539A GLY 2.9 38.9 + - - +
543A LEU* 3.3 35.0 - - - +
551A SER* 3.3 19.5 + - - +
553A SER 3.5 3.8 - - - +
554A LEU* 1.3 76.4 - - - +
556A GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ILE* 4.4 2.9 - - - -
411A GLY* 3.1 4.0 - - - -
412A SER* 2.9 47.6 + - - +
413A SER 5.0 0.2 - - - -
414A SER* 2.7 29.7 - - - -
415A LEU 4.7 0.4 + - - -
418A SER* 3.9 7.3 + - - -
419A HIS* 2.9 29.6 + - - +
536A GLN* 3.6 22.4 + - - +
537A ILE 3.3 10.3 - - - +
538A ALA* 4.2 0.2 - - - +
555A ARG* 1.3 74.5 - - - +
557A ALA* 1.3 62.2 + - - +
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Residues in contact with ALA 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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408A ILE* 4.0 10.5 - - + -
410A GLY 4.3 1.3 - - - +
411A GLY* 3.9 11.0 - - - -
536A GLN* 3.4 9.9 - - - +
537A ILE* 3.1 40.1 + - + +
556A GLU* 1.3 78.8 - - - +
558A LEU* 1.3 62.4 + - - +
591A SER* 3.8 28.0 - - - +
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Residues in contact with LEU 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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534A LYS* 4.6 24.7 - - + +
535A CYS 3.2 20.0 - - - +
536A GLN* 3.9 26.9 - - + +
557A ALA* 1.3 74.4 - - - +
559A VAL* 1.3 65.5 + - - +
586A TYR* 3.0 25.6 + - - +
590A LYS* 5.4 0.3 - - - -
591A SER* 3.4 4.7 + - - -
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Residues in contact with VAL 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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534A LYS* 4.5 3.1 - - - -
535A CYS* 2.8 37.2 + - - +
537A ILE* 3.9 34.1 - - + -
557A ALA 5.0 0.2 - - - -
558A LEU* 1.3 81.0 - - - +
560A PRO* 1.3 64.8 - - - +
584A ALA* 4.2 8.3 - - + -
585A GLY* 3.7 23.1 - - - +
586A TYR* 4.3 1.1 - - + -
591A SER* 4.1 15.7 - - - +
592A ASP* 4.9 1.6 - - - +
602A LEU* 3.6 29.8 - - + -
631A TYR* 4.3 3.6 - - - +
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Residues in contact with PRO 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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532A GLY* 3.9 19.5 - - - +
533A HIS 3.3 8.3 - - - +
534A LYS* 4.1 14.6 - - + +
559A VAL* 1.3 84.0 - - + +
561A LEU* 1.3 65.5 + - - +
562A VAL* 3.3 1.8 + - + +
584A ALA* 3.3 1.9 - - - -
585A GLY 2.8 43.5 + - - +
586A TYR* 3.3 34.5 - - + +
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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