Contacts of the strand formed by residues 328 - 335 (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 328 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231E HIS* 2.9 34.3 + - - -
322E LEU* 3.6 25.5 + - + +
323E THR* 3.5 26.9 - - + -
326E HIS* 2.8 22.8 + - - +
327E THR* 1.3 78.8 + - - +
329E GLN* 1.3 57.1 + - - +
347E ALA 4.4 1.3 - - - -
348E SER* 3.2 5.4 - - - -
349E PHE* 2.4 38.4 + - + +
474E LEU* 4.0 20.9 - - + +
475E ARG 3.4 11.5 + - - +
476E PRO* 4.1 13.3 - - - +
477E LYS* 4.6 1.7 + - - -
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Residues in contact with GLN 329 (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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270E TRP* 3.3 11.8 - - + -
328E GLN* 1.3 74.9 - - - +
330E VAL* 1.3 59.3 + - - +
345E GLN* 4.2 7.4 - - - +
346E TYR 3.4 11.2 - - - +
347E ALA* 3.3 23.4 - - - +
349E PHE* 4.1 1.3 - - - +
474E LEU* 3.5 2.1 - - - -
475E ARG* 2.7 92.4 + - + +
476E PRO 2.9 20.8 + - - +
477E LYS* 3.9 17.7 + - - +
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Residues in contact with VAL 330 (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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270E TRP* 4.2 1.3 - - - -
329E GLN* 1.3 74.6 - - - +
331E LEU* 1.3 70.8 + - - +
332E PHE* 3.3 33.2 - - + -
345E GLN* 3.0 6.6 - - - +
346E TYR* 2.9 51.2 + - + +
349E PHE* 3.4 31.7 - - + +
362E VAL* 4.4 1.8 - - + -
472E MET* 3.6 22.7 - - + -
473E LYS 3.2 11.9 - - - +
474E LEU* 3.9 2.2 - - + -
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Residues in contact with LEU 331 (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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265E SER* 5.1 0.4 - - - -
266E HIS* 3.5 27.1 - - + +
270E TRP* 3.5 46.2 - - + +
330E VAL* 1.3 77.3 - - - +
332E PHE* 1.3 71.1 + - - +
333E ASP* 3.0 24.6 + - - +
343E TYR* 4.2 6.1 - - + -
344E ALA 3.7 1.1 - - - +
345E GLN* 3.6 32.5 - - + +
471E ALA 3.7 1.6 - - - +
472E MET 3.8 0.2 - - - -
473E LYS* 2.8 41.8 + - + +
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Residues in contact with PHE 332 (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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330E VAL* 3.3 24.2 - - + -
331E LEU* 1.3 77.4 - - - +
333E ASP* 1.3 62.0 + - - +
334E MET* 3.9 16.7 + - + +
342E VAL 3.8 0.3 - - - +
343E TYR* 3.1 27.2 - - - +
344E ALA* 2.8 25.3 + - + +
346E TYR* 4.6 2.2 - + - -
349E PHE* 5.4 1.6 - + - -
373E LEU* 3.9 31.9 - - + -
422E TRP* 4.0 17.5 - + - -
423E TRP* 6.1 0.2 - + - -
432E PRO* 4.5 2.2 - - + -
457E TRP* 3.4 29.8 - + + -
470E MET* 4.5 8.5 - - - -
471E ALA 3.3 7.0 - - - +
472E MET* 3.3 38.8 - - + -
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Residues in contact with ASP 333 (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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265E SER* 3.9 7.6 + - - -
266E HIS* 3.8 17.8 + - - -
331E LEU* 3.0 37.4 - - - +
332E PHE* 1.3 72.1 - - - +
334E MET* 1.3 60.4 + - - +
342E VAL 3.7 4.7 - - - +
343E TYR* 3.9 12.3 - - + -
469E GLN* 4.0 1.3 - - - +
470E MET* 3.4 3.2 + - - -
471E ALA* 3.0 33.6 + - + +
473E LYS* 3.2 30.1 + - - +
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Residues in contact with MET 334 (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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332E PHE* 3.9 20.2 - - + +
333E ASP* 1.3 74.4 - - - +
335E SER* 1.3 62.6 + - - +
341E SER* 3.3 5.0 - - - -
342E VAL* 3.0 53.4 + - + +
369E ALA* 3.8 11.2 - - + -
457E TRP* 3.3 71.3 - - + -
460E TRP* 4.3 9.2 - - + -
467E MET* 4.0 11.9 - - + +
469E GLN* 2.9 11.9 - - - +
470E MET* 4.0 10.8 - - + -
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Residues in contact with SER 335 (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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334E MET* 1.3 75.8 + - - +
336E ASP* 1.3 60.6 + - - +
340E SER 3.3 6.5 - - - -
341E SER* 2.6 22.6 + - - +
460E TRP* 4.3 4.0 - - - -
467E MET* 3.6 3.3 - - - +
468E ARG* 2.8 49.0 + - - -
469E GLN* 2.7 36.0 + - - +
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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