Contacts of the helix formed by residues 298 - 307 (chain C) in PDB entry 5T0H
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 ILE 298 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C SER 5.6 0.2 - - - +
254C ILE* 3.7 37.7 - - + +
257C SER* 4.4 21.1 - - - +
259C LEU* 6.5 0.7 - - + -
297C ARG* 1.3 91.8 - - + +
299C ASP* 1.3 64.9 + - + +
300C ILE 2.8 0.7 + - - -
301C LEU* 2.4 40.0 + - - +
302C ASP* 2.8 9.8 + - + -
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Residues in contact with ASP 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ILE* 5.1 4.3 - - - +
253C SER 5.2 2.8 - - - +
256C SER* 4.5 10.9 + - - -
257C SER* 5.2 10.7 - - - -
266C ASP* 3.2 27.0 - - - +
270C GLN* 4.7 6.1 + - - +
295C THR* 3.7 22.6 - - + +
297C ARG 2.7 5.1 + - - -
298C ILE* 1.3 85.0 - - - +
300C ILE* 1.3 48.4 + - - +
302C ASP* 3.1 25.0 - - + +
303C SER* 2.4 41.5 + - - -
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Residues in contact with ILE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LEU* 4.2 14.8 - - + -
189C TYR* 3.5 36.6 - - + -
295C THR* 3.6 27.4 - - - +
296C ASN 3.4 25.1 - - - +
297C ARG* 3.3 20.9 + - - +
298C ILE 2.8 3.8 + - - -
299C ASP* 1.3 74.4 - - - +
301C LEU* 1.3 62.7 + - + +
303C SER* 3.2 26.4 + - - +
304C ALA* 3.4 5.7 + - - +
314C LYS* 4.0 26.2 + - - +
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Residues in contact with LEU 301 (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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432B GLU* 4.9 16.8 - - - +
433B GLY* 5.6 5.2 - - - -
297C ARG* 4.7 26.2 - - + +
298C ILE* 2.4 28.8 + - - +
300C ILE* 1.3 72.8 - - + +
302C ASP* 1.3 58.3 + - - +
303C SER 3.2 0.2 - - - -
304C ALA* 3.0 26.6 + - + +
305C LEU* 3.4 4.5 + - - +
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Residues in contact with ASP 302 (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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266C ASP* 4.1 9.0 - - - +
270C GLN* 4.3 7.1 - - - +
298C ILE* 2.8 7.4 + - + +
299C ASP* 3.4 33.7 - - - +
301C LEU* 1.3 73.4 - - - +
303C SER* 1.3 64.5 + - - +
305C LEU* 3.1 40.5 + - - +
306C LEU* 3.2 16.6 + - - +
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Residues in contact with SER 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LEU* 5.2 9.8 - - - +
270C GLN* 4.7 11.4 + - - -
295C THR* 5.0 2.1 + - - -
299C ASP* 2.4 34.8 + - - +
300C ILE* 3.2 25.5 - - - +
301C LEU 3.2 0.2 - - - -
302C ASP* 1.3 71.5 - - - +
304C ALA* 1.3 47.9 + - - +
306C LEU* 2.9 12.7 + - - +
307C ARG* 2.6 45.4 + - - +
314C LYS* 5.4 7.4 - - - -
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Residues in contact with ALA 304 (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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429B LYS* 5.0 2.0 - - - +
433B GLY* 3.7 32.3 - - - -
300C ILE 3.4 5.5 + - - +
301C LEU* 3.0 18.8 + - + +
303C SER* 1.3 73.8 - - - +
305C LEU* 1.3 61.6 + - - +
307C ARG* 2.9 34.0 + - - +
308C PRO* 3.7 1.7 - - - +
314C LYS* 6.0 1.7 - - - +
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Residues in contact with LEU 305 (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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301C LEU 3.4 4.4 + - - +
302C ASP* 3.1 28.1 + - - +
304C ALA* 1.3 78.2 - - - +
306C LEU* 1.3 77.2 + - + +
307C ARG 3.5 0.2 + - - -
308C PRO* 4.0 7.1 - - - +
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Residues in contact with LEU 306 (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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270C GLN* 3.2 45.1 - - + +
273C MET* 4.0 8.7 - - + -
274C LEU* 3.7 35.0 - - + +
302C ASP* 3.2 24.9 + - - +
303C SER* 2.9 9.9 + - - +
305C LEU* 1.3 94.2 - - + +
307C ARG* 1.3 80.5 + - - +
308C PRO* 3.5 5.5 - - - +
310C ARG* 2.8 14.0 - - - +
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Residues in contact with ARG 307 (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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429B LYS* 3.0 34.0 + - - +
433B GLY 5.4 1.4 - - - -
273C MET* 3.4 22.1 - - - +
274C LEU* 4.1 8.7 - - - +
277C LEU* 3.2 29.1 - - - +
303C SER* 2.6 25.5 + - - +
304C ALA* 2.9 21.7 + - - +
306C LEU* 1.3 118.5 + - + +
308C PRO* 1.3 57.4 - - - +
309C GLY* 3.1 5.4 - - - +
310C ARG 2.9 22.2 + - - +
311C ILE 3.2 14.5 + - - +
312C ASP* 3.1 30.9 - - + +
314C LYS* 6.4 1.6 - - + -
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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