Contacts of the strand formed by residues 446 - 451 (chain A) in PDB entry 1LB6
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 HIS 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A THR* 3.4 0.3 - - - -
434A ILE* 2.8 38.4 + - + +
444A GLN 3.9 0.2 + - - -
445A ASN* 1.3 75.2 - - - +
447A GLU* 1.3 62.1 + - - +
448A GLU* 5.0 9.9 - - - -
476A PHE* 2.8 42.4 - + - -
477A MET* 3.5 53.8 - - + +
481A ALA* 5.2 2.2 - - + +
485A ARG* 5.5 5.8 - - - -
487A PHE* 4.2 4.9 - + + -
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Residues in contact with GLU 447 (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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431A ARG* 2.7 44.9 + - + +
432A LEU 3.0 18.8 - - - +
433A THR* 2.5 35.4 + - + +
445A ASN* 3.9 9.0 + - + +
446A HIS* 1.3 78.3 + - - +
448A GLU* 1.3 76.2 + - - +
449A ILE* 4.2 6.2 - - + +
476A PHE* 4.1 2.5 - - - -
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Residues in contact with GLU 448 (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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430A ILE 4.0 0.7 - - - +
431A ARG* 3.6 2.3 - - - +
432A LEU* 2.9 30.6 + - - +
446A HIS* 5.0 5.6 - - + -
447A GLU* 1.3 82.9 - - - +
449A ILE* 1.3 66.5 + - - +
450A MET* 4.3 0.4 - - - -
473A TYR* 3.5 29.2 + - + -
476A PHE* 3.6 26.9 - - + +
601B LYS* 5.3 8.0 - - - +
602B GLN* 3.1 44.2 + - - +
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Residues in contact with ILE 449 (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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429A THR* 3.3 30.5 - - + -
430A ILE 3.5 8.1 - - - +
431A ARG* 3.8 45.3 - - + +
447A GLU* 4.2 6.7 - - + +
448A GLU* 1.3 81.0 + - - +
450A MET* 1.3 60.7 + - - +
473A TYR* 3.5 6.0 + - - -
601B LYS* 4.6 21.5 + - - +
604B PRO* 5.5 0.9 - - - +
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Residues in contact with MET 450 (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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411A VAL* 3.8 17.7 - - + -
429A THR* 3.3 5.1 - - - +
430A ILE* 2.9 57.3 + - + +
432A LEU* 3.8 20.0 - - + -
449A ILE* 1.3 73.0 - - - +
451A ASP* 1.3 62.6 + - - +
452A ALA 3.8 0.3 + - - -
459A PHE* 5.5 0.9 - - + -
471A PHE* 3.5 44.6 - - + +
472A GLY* 4.1 4.3 - - - -
473A TYR* 3.3 37.0 - - + +
604B PRO* 3.8 20.0 - - + -
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Residues in contact with ASP 451 (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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428A GLY 3.6 4.9 - - - +
429A THR* 2.8 32.4 + - - +
450A MET* 1.3 76.6 - - - +
452A ALA* 1.3 68.7 + - - +
453A LYS* 3.6 7.4 + - + +
471A PHE* 3.8 14.9 - - - -
604B PRO* 5.3 1.1 - - - +
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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