Contacts of the strand formed by residues 312 - 314 (chain H) 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 TYR 312 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260H PHE* 3.1 27.9 + - + -
272H VAL* 2.5 49.3 + - + +
273H VAL 4.1 4.7 - - - -
274H GLN* 3.2 5.0 - - - +
275H ASN* 3.1 33.1 + - + -
283H PHE* 3.8 12.8 - - - -
293H GLU* 5.0 0.4 - - + -
294H PHE* 3.1 14.8 - - - +
295H GLY* 3.8 2.0 - - - -
296H ASN 3.2 27.1 - - - +
297H ILE* 3.4 39.0 - - + -
310H GLY 3.7 8.7 - - - -
311H GLU* 1.3 74.8 - - - +
313H TRP* 1.3 63.0 - - - +
314H LEU* 3.3 26.0 - - + -
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Residues in contact with TRP 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 3.5 10.3 - - + -
274H GLN* 3.3 37.5 - - + -
283H PHE* 4.4 1.8 - - + -
290H TYR* 3.0 51.3 + + - -
293H GLU* 2.8 18.8 - - - +
294H PHE* 2.8 37.6 + + + -
312H TYR* 1.3 74.1 - - - +
314H LEU* 1.3 87.5 + - - +
315H GLY* 4.1 0.4 - - - -
316H THR* 3.0 21.2 + - - +
319H VAL* 5.4 2.0 - - + -
395H PHE* 3.8 15.0 - + - -
422H TRP* 4.5 6.1 - + - -
423H TRP* 3.8 28.9 - + - -
433H ASN* 3.3 27.6 - - - -
472H MET* 4.5 6.1 - - - -
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Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H TYR* 3.9 24.0 - - + +
258H LYS 4.1 8.1 - - - +
259H VAL* 3.7 30.5 - - + -
271H THR* 4.8 5.4 - - + -
273H VAL* 2.8 39.9 + - + +
293H GLU* 3.4 18.2 - - - +
297H ILE* 5.3 0.2 - - + -
312H TYR* 3.3 15.6 - - + -
313H TRP* 1.3 83.3 + - - +
315H GLY* 1.3 69.0 + - - +
318H THR* 3.9 26.9 - - + +
319H VAL* 3.8 7.4 - - + +
322H LEU* 5.3 4.0 - - + -
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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
------------------------------------------------------------
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