Contacts of the strand formed by residues 469 - 475 (chain E) in PDB entry 1LWU
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 GLN 469 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276E ARG* 3.6 6.7 - - - +
277E VAL* 3.4 28.4 - - + +
333E ASP 4.3 1.3 - - - +
334E MET* 2.9 7.8 - - - +
335E SER* 2.7 55.5 + - - +
467E MET* 3.3 3.6 - - - +
468E ARG* 1.3 111.6 + - - +
470E MET* 1.3 60.8 + - - +
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Residues in contact with MET 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E GLN* 3.8 6.0 + - - +
275E ASN* 3.4 0.2 - - - -
276E ARG* 2.5 45.1 + - + +
332E PHE* 4.5 5.4 - - - -
333E ASP 3.4 5.4 - - - +
334E MET* 4.0 27.6 - - - -
432E PRO* 3.5 35.0 - - + -
455E VAL* 3.6 30.1 - - + -
456E VAL 4.4 8.1 - - - +
457E TRP* 3.8 25.6 - - + -
467E MET* 4.1 9.2 - - + -
469E GLN* 1.3 75.6 - - - +
471E ALA* 1.3 74.4 + - - +
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Residues in contact with ALA 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E VAL* 4.8 2.0 - - + -
274E GLN* 3.1 15.9 - - - +
275E ASN* 3.3 19.1 - - + +
331E LEU 3.7 0.5 - - - +
332E PHE* 3.3 10.4 - - - +
333E ASP* 3.0 32.8 + - + +
470E MET* 1.3 80.9 - - - +
472E MET* 1.3 60.7 + - - +
473E LYS* 4.1 21.1 - - - -
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Residues in contact with MET 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E VAL* 3.5 3.1 - - - -
273E VAL* 2.8 40.7 + - + -
274E GLN* 2.8 30.4 + - + +
313E TRP* 4.5 11.7 - - - -
319E VAL* 6.0 0.2 - - + -
330E VAL* 3.6 25.1 - - + -
331E LEU 3.9 2.7 - - - -
332E PHE* 3.3 35.0 - - + -
349E PHE* 3.6 29.6 - - + -
422E TRP* 4.1 20.9 - - + -
423E TRP* 4.3 7.0 - - + -
432E PRO* 5.4 1.8 - - + -
471E ALA* 1.3 72.8 - - - +
473E LYS* 1.3 56.4 + - - +
474E LEU* 4.5 4.5 - - + -
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Residues in contact with LYS 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ASP* 2.6 35.8 + - - +
265E SER* 3.8 4.2 + - - -
270E TRP* 3.4 28.6 - - + -
271E THR 3.4 4.7 - - - +
272E VAL* 3.8 21.5 - - + -
330E VAL* 3.2 7.1 - - - +
331E LEU* 2.8 43.8 + - + +
333E ASP* 3.2 43.5 + - + +
471E ALA* 4.4 12.8 - - + +
472E MET* 1.3 80.6 - - - +
474E LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E HIS* 2.8 18.2 + - + -
270E TRP* 3.4 4.2 - - - -
271E THR* 2.8 28.5 + - - +
273E VAL* 3.4 25.4 - - + -
319E VAL* 3.7 19.7 - - + -
322E LEU* 3.7 21.8 - - + -
323E THR* 4.7 1.6 - - + -
328E GLN* 4.0 20.6 - - + +
329E GLN 3.5 0.9 - - - -
330E VAL* 3.9 14.6 - - + -
349E PHE* 3.6 32.5 - - + -
472E MET* 4.5 2.7 - - + -
473E LYS* 1.3 81.0 - - - +
475E ARG* 1.3 62.5 + - - +
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Residues in contact with ARG 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E HIS* 3.1 1.3 - - - -
233E GLU* 3.3 21.4 + - - +
266E HIS* 3.2 24.4 + - - +
267E GLY* 4.4 4.8 + - - -
268E GLY 3.6 19.0 + - - -
269E GLY 3.8 6.3 - - - +
270E TRP* 3.3 33.0 - - + +
328E GLN* 3.4 5.7 - - - -
329E GLN* 2.7 67.1 + - + +
345E GLN* 4.8 3.6 + - - -
474E LEU* 1.3 77.2 - - - +
476E PRO* 1.3 75.3 - - + +
477E LYS 4.7 3.9 + - - +
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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