Contacts of the strand formed by residues 555 - 559 (chain A) in PDB entry 1U1H
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 LYS 555 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A THR* 3.2 35.2 + - - +
436A THR 3.4 7.7 + - - -
437A ILE* 5.8 0.8 - - - +
485A VAL* 3.7 13.2 - - + +
486A LEU 3.0 21.9 + - - +
487A VAL* 3.8 18.4 - - + -
488A HIS* 4.7 3.1 + - - -
543A SER* 4.9 0.2 + - - -
553A PRO 4.1 0.4 + - - -
554A MSE 1.3 92.9 - - - +
556A GLY* 1.3 65.0 + - - +
557A MSE 4.1 5.7 + - + +
599A ILE* 4.5 1.1 - - - -
601A VAL* 3.0 22.9 - - + +
603A GLN* 2.7 42.2 + - + +
645A HIS* 4.3 22.3 + - - -
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Residues in contact with GLY 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A SER* 4.3 12.8 - - - -
555A LYS* 1.3 76.0 - - - +
557A MSE 1.3 61.2 + - - +
594A LEU* 4.5 9.0 - - - -
599A ILE* 3.8 12.4 - - - +
601A VAL 2.7 15.3 + - - -
602A ILE* 4.2 5.8 - - - -
603A GLN* 2.8 31.5 + - - +
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Residues in contact with MSE 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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437A ILE 3.7 4.0 - - - +
438A GLY* 4.4 1.1 - - - -
487A VAL* 4.4 11.4 - - + -
488A HIS* 4.0 16.3 - - + +
490A GLU* 3.6 15.5 - - - +
493A ARG* 3.0 45.0 + - - +
500A PHE* 3.5 0.7 - - - -
539A THR* 4.0 5.9 + - - +
543A SER* 4.7 1.0 + - - -
555A LYS* 4.6 4.5 - - + +
556A GLY* 1.3 77.3 - - - +
558A LEU* 1.3 76.8 + - - +
559A THR* 5.9 0.7 - - - +
594A LEU* 4.9 0.2 - - - +
603A GLN* 3.4 33.7 - - - +
605A ASP* 2.9 17.7 - - - +
772A MET* 2.8 31.0 - - + +
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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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500A PHE* 3.7 23.1 - - + -
538A MSE 5.0 1.6 - - + -
539A THR* 3.7 15.5 - - - +
557A MSE 1.3 86.7 - - - +
559A THR* 1.3 62.1 + - - +
587A ILE* 3.9 20.9 - - + -
590A GLU* 4.1 11.7 - - + -
591A VAL* 3.5 36.8 - - + +
594A LEU* 3.9 23.1 - - + -
602A ILE* 4.3 5.4 - - + -
603A GLN 2.9 11.3 + - - +
604A ILE* 3.2 8.9 - - + -
605A ASP* 2.9 31.5 + - - +
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Residues in contact with THR 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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496A MSE 3.1 42.2 + - + +
497A VAL* 4.7 2.9 - - + -
500A PHE* 3.3 17.1 - - - -
557A MSE 5.9 0.7 - - - +
558A LEU* 1.3 73.7 - - - +
560A GLY* 1.3 76.4 + - - +
563A THR* 3.6 31.2 - - + -
564A ILE* 3.7 21.4 - - + +
587A ILE* 4.1 13.5 - - - +
604A ILE* 4.3 1.8 - - - -
605A ASP* 3.4 8.8 + - - +
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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