Contacts of the strand formed by residues 297 - 300 (chain C) in PDB entry 3LUE
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 THR 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ILE* 3.4 10.7 - - + +
153C MET* 5.5 2.9 - - + -
278C THR* 3.9 26.8 - - + +
282C ILE* 5.1 1.9 - - - +
293C LEU 3.2 14.9 + - - -
294C TYR* 3.8 10.0 + - - -
296C ASN* 1.3 73.8 - - - +
298C VAL* 1.3 53.9 + - - +
299C LEU* 4.7 12.6 - - + -
313C MET* 5.2 0.9 - - + -
317C ILE* 4.2 5.6 - - + +
327C ILE* 5.3 0.5 - - - +
328C LYS 3.2 11.4 + - - -
329C ILE* 3.2 25.7 - - + +
330C ILE* 2.5 35.5 + - - +
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 4.9 0.2 - - - -
45A VAL* 3.0 38.1 - - + +
46A GLY* 4.2 0.4 - - - -
141C SER* 6.2 0.2 - - - -
145C SER* 5.2 4.5 - - - +
147C ARG* 4.2 18.4 - - - +
151C ILE 2.9 12.2 + - - +
152C VAL* 3.2 7.7 - - + -
153C MET* 2.8 28.6 + - - +
296C ASN 4.3 5.6 - - - +
297C THR* 1.3 76.7 - - - +
299C LEU* 1.3 75.6 + - - +
300C SER* 5.4 1.6 - - - -
330C ILE* 3.4 29.8 - - + +
332C PRO* 4.3 9.4 - - + -
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C MET* 3.5 14.6 - - + +
297C THR* 4.7 10.8 - - + -
298C VAL* 1.3 89.0 - - - +
300C SER* 1.3 64.8 + - - +
304C THR* 3.8 20.2 - - + +
309C ILE* 3.8 35.2 - - + +
310C ALA* 4.4 15.0 - - - +
313C MET* 3.9 31.4 - - + -
329C ILE* 4.6 8.3 - - + -
330C ILE 3.1 14.6 + - - +
331C ALA* 4.6 7.2 - - + -
332C PRO* 4.2 3.8 - - - +
335C ARG* 3.9 18.8 - - - +
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Residues in contact with SER 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER* 2.8 31.3 + - - -
152C VAL* 3.5 9.6 - - - +
153C MET 2.9 8.2 + - - +
154C ASP* 2.6 30.5 + - - -
155C SER 3.0 22.1 + - - -
298C VAL* 4.1 1.8 + - - -
299C LEU* 1.3 76.4 - - - +
301C GLY* 1.3 59.1 + - - +
304C THR* 3.1 9.4 - - - +
335C ARG* 3.8 8.3 - - - -
338C SER* 5.0 2.5 - - - -
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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