Contacts of the strand formed by residues 555 - 560 (chain A) in PDB entry 1L5G
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 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A LEU* 4.2 11.2 - - + -
473A PHE* 5.3 2.0 - - + -
499A LEU* 5.2 0.2 - - - -
500A ASP* 3.4 32.8 - - + +
510A ARG* 3.1 34.1 - - + +
511A ALA* 3.7 18.6 - - + -
542A LEU* 3.4 32.5 - - + -
552A LEU* 5.3 0.4 - - + -
554A PRO* 1.3 69.2 - - - +
556A THR* 1.3 56.1 + - - +
557A ILE* 3.5 9.2 - - + +
589A GLN* 3.3 0.3 - - - -
590A ALA* 2.5 53.4 + - + +
592A ILE* 4.0 14.4 - - + +
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Residues in contact with THR 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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498A LEU 3.4 3.1 - - - +
500A ASP* 3.1 19.7 + - - +
501A LYS* 3.3 23.0 + - - +
502A LEU* 3.8 25.1 + - + +
554A PRO* 3.3 10.4 + - + +
555A ILE* 1.3 72.5 - - - +
557A ILE* 1.3 62.8 + - - +
558A PHE* 3.8 0.8 + - - -
587A SER* 5.3 9.0 - - - -
588A ARG 3.5 4.9 - - - -
589A GLN* 3.2 34.3 - - + +
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Residues in contact with ILE 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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447A LEU* 3.5 28.4 - - + +
449A VAL* 4.5 15.0 - - + -
473A PHE* 4.8 10.3 - - + -
475A VAL* 4.2 15.3 - - + -
497A LEU* 4.8 6.1 - - + -
498A LEU 3.1 11.7 - - - +
499A LEU* 3.8 26.7 - - + -
500A ASP 5.2 0.7 - - - +
555A ILE* 3.5 21.1 - - + +
556A THR* 1.3 73.0 - - - +
558A PHE* 1.3 65.6 + - - +
587A SER* 3.2 7.4 - - - -
588A ARG* 2.6 43.6 + - + +
590A ALA* 4.2 15.0 - - + +
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Residues in contact with PHE 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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447A LEU* 4.6 0.4 - - - -
496A GLU 3.2 6.8 - - - +
497A LEU* 3.4 1.5 - - - -
498A LEU* 2.7 65.7 + - + +
501A LYS* 4.7 13.7 - - + -
556A THR* 3.8 1.1 + - - +
557A ILE* 1.3 73.8 - - - +
559A MET* 1.3 60.6 + - - +
560A GLU* 3.6 29.2 - - + -
585A ASN* 3.4 35.4 - - + -
587A SER* 3.2 22.9 - - - +
1F NAG 3.3 35.4 - - + -
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Residues in contact with MET 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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445A ALA* 3.3 21.3 - - + -
446A GLY 3.1 27.8 - - - +
447A LEU* 3.6 15.6 - - + +
477A PHE* 3.7 17.5 - - + -
478A CYS 4.7 1.6 - - - +
479A LEU* 4.4 4.9 - - + -
495A VAL* 3.6 23.6 - - + -
496A GLU 3.4 3.6 - - - +
497A LEU* 4.7 3.8 - - + +
558A PHE* 1.3 73.0 - - - +
560A GLU* 1.3 61.2 + - - +
561A TYR* 3.3 37.7 - - + -
584A ALA 3.9 0.5 - - - +
585A ASN* 2.9 6.5 - - - +
586A ILE* 2.8 55.5 + - + +
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Residues in contact with GLU 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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495A VAL* 3.3 5.0 - - - +
496A GLU* 2.8 60.4 + - + +
498A LEU* 4.7 6.2 - - - +
558A PHE* 3.6 18.5 + - + -
559A MET* 1.3 74.3 - - - +
561A TYR* 1.3 68.5 + - - +
584A ALA* 3.4 7.4 - - + -
585A ASN* 3.4 17.5 - - - +
1F NAG 3.0 24.9 + - - +
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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