Contacts of the strand formed by residues 296 - 299 (chain C) in PDB entry 5JLH
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 296 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ILE* 3.2 30.4 - - + +
152C MET* 4.9 4.9 - - + -
277C THR* 4.9 12.3 - - + +
281C ILE* 5.0 0.9 - - - +
292C LEU 3.3 7.4 + - - -
293C TYR* 4.0 7.1 + - - -
294C ALA 3.7 2.2 - - - -
295C ASN* 1.3 72.7 - - - +
297C VAL* 1.3 64.8 + - - +
298C LEU* 4.6 10.5 - - + -
312C MET* 5.4 7.0 - - + -
316C ILE* 5.2 5.6 - - + +
326C ILE* 5.5 0.5 - - - +
327C LYS 3.8 3.2 + - - -
328C ILE* 3.7 29.9 - - + +
329C ILE* 2.8 31.0 + - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER* 4.6 12.1 - - - +
141C LEU* 4.8 7.0 - - + -
144C SER* 3.8 21.8 - - - +
146C ARG* 3.8 17.9 - - - -
149C GLY* 5.1 0.2 - - - -
150C ILE 3.0 6.7 + - - -
151C VAL* 3.3 24.2 - - + +
152C MET* 2.8 27.9 + - - +
295C ASN 3.2 14.6 + - - +
296C THR* 1.3 72.6 - - - +
298C LEU* 1.3 75.8 - - - +
329C ILE* 3.4 21.8 - - + +
331C PRO* 5.0 2.2 - - + -
337C SER* 6.4 0.4 - - - -
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C MET* 3.5 32.8 - - + -
273C ILE* 6.4 0.4 - - + -
296C THR* 4.6 10.5 - - + -
297C VAL* 1.3 83.3 - - - +
299C SER* 1.3 61.8 + - - +
303C THR* 4.0 22.4 - - + +
308C ILE* 4.1 25.1 - - + -
309C ALA* 4.4 13.2 - - + +
312C MET* 5.0 14.1 - - + -
328C ILE* 4.5 10.3 - - + -
329C ILE 3.5 5.5 + - - -
330C ALA* 3.7 27.4 - - + -
331C PRO* 4.0 6.8 - - - +
334C ARG* 3.8 18.5 - - - +
337C SER* 5.0 1.0 + - - -
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Residues in contact with SER 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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137C ALA* 5.5 0.3 - - - -
140C SER* 3.7 32.7 + - - -
151C VAL* 4.1 1.9 - - - +
152C MET 2.8 9.3 + - - +
153C ASP* 3.4 26.7 + - - +
154C SER 3.4 16.8 + - - +
298C LEU* 1.3 75.2 - - - +
300C GLY* 1.3 65.2 + - - +
303C THR* 2.9 14.2 + - - +
334C ARG* 4.1 6.5 - - - -
337C SER* 4.3 7.6 - - - -
338C VAL* 4.6 6.9 - - - +
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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