Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 4JYH
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 LEU 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PHE* 3.0 12.2 + - - +
297A PRO* 1.3 88.6 - - + +
299A THR* 1.3 63.8 + - - +
300A ASP 3.5 1.8 - - - -
301A LEU* 3.3 17.9 + - + +
302A VAL* 3.1 29.0 + - + +
380A ILE* 4.7 4.5 - - + +
383A LYS* 3.1 48.2 - - + +
384A GLY* 3.6 6.7 - - - +
387A ARG* 3.5 33.7 - - + -
501A JYH 4.9 5.6 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ARG* 5.1 3.8 - - - +
287A ARG* 3.5 41.5 - - + +
290A MET* 4.7 0.2 - - + -
291A HIS* 3.1 17.7 - - + +
295A PHE* 3.1 27.0 + - + +
296A GLY 2.6 22.0 + - - -
297A PRO 3.3 1.2 - - - -
298A LEU* 1.3 78.1 - - - +
300A ASP* 1.3 67.7 + - - +
302A VAL* 3.0 4.9 + - - +
303A PHE* 3.0 36.2 + - + -
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ARG* 4.4 14.3 + - - -
287A ARG* 3.3 40.0 + - - +
297A PRO 5.0 2.3 + - - +
298A LEU 3.5 0.4 - - - -
299A THR* 1.3 76.7 - - - +
301A LEU* 1.3 57.2 + - - +
303A PHE* 3.8 1.6 - - - +
304A THR* 2.8 42.2 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A PRO 5.5 1.1 + - - +
298A LEU* 3.3 22.6 + - + +
299A THR 3.2 0.2 - - - -
300A ASP* 1.3 78.9 - - - +
302A VAL* 1.3 60.4 + - + +
304A THR* 3.7 7.5 + - + -
305A PHE* 3.3 21.8 + - - +
379A SER* 5.9 0.2 - - - +
380A ILE* 4.3 26.3 - - + +
383A LYS* 3.5 37.7 - - + -
333B GLN* 6.1 1.3 - - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ILE* 4.9 6.1 - - + -
266A ILE* 4.7 6.1 - - + -
267A CYS* 3.4 26.0 - - - -
277A MET* 4.3 8.2 - - + +
295A PHE* 3.5 35.7 - - + -
298A LEU* 3.2 19.7 - - + +
299A THR 3.0 7.7 + - - +
301A LEU* 1.3 79.3 - - + +
303A PHE* 1.3 60.3 - - + +
305A PHE* 3.6 3.5 + - - +
306A ALA* 3.3 14.6 + - - +
380A ILE* 4.1 22.2 - - + -
501A JYH 4.4 11.9 - - + -
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TYR* 3.5 33.4 - + + -
275A ASP* 3.6 20.0 - - - -
276A THR* 4.5 1.3 - - - -
277A MET* 3.7 25.4 - - + -
286A ASN 4.4 0.7 - - - -
287A ARG* 3.5 50.5 - - + +
290A MET* 3.7 31.4 - - + -
295A PHE* 4.8 3.6 - + - -
299A THR* 3.0 34.5 + - + +
300A ASP 3.8 5.6 - - - +
302A VAL* 1.3 78.3 - - + +
304A THR* 1.3 66.6 + - - +
306A ALA* 2.9 17.6 + - - +
307A ASN* 3.0 17.1 + - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ARG* 5.5 2.1 + - - +
300A ASP* 2.8 29.3 + - - +
301A LEU* 3.9 9.9 - - + -
303A PHE* 1.3 72.1 - - - +
305A PHE* 1.3 61.2 + - - +
307A ASN* 3.1 22.4 + - + +
308A GLN* 3.1 34.5 + - + +
333B GLN* 3.8 26.7 + - - +
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ILE* 4.1 2.2 - - + -
264A LEU* 4.7 7.4 - - + -
267A CYS* 3.4 35.7 - - + -
301A LEU 3.3 9.1 + - - +
302A VAL 3.7 2.2 - - - +
303A PHE 3.2 0.4 - - - -
304A THR* 1.3 79.2 - - - +
306A ALA* 1.3 60.5 + - - +
308A GLN* 3.3 20.4 + - + +
309A LEU* 3.5 36.3 + - + +
373A LYS* 4.0 11.9 - - + -
376A ASP* 3.5 39.5 - - + -
377A LEU* 3.9 32.3 - - + -
380A ILE* 3.6 27.1 - - + -
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A CYS* 3.9 23.7 - - - +
270A TYR* 3.8 31.9 - - + -
277A MET* 3.9 7.4 - - + -
302A VAL 3.3 10.5 + - - +
303A PHE 2.9 12.0 + - - +
305A PHE* 1.3 80.4 - - - +
307A ASN* 1.3 58.8 + - - +
309A LEU* 3.5 10.5 + - - +
310A LEU* 3.4 20.8 - - - +
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Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TYR* 3.3 32.9 + - - -
272A PRO* 5.1 3.4 - - - +
287A ARG* 4.7 7.1 + - - -
303A PHE 3.0 16.1 + - - +
304A THR* 3.1 14.5 + - + +
306A ALA* 1.3 73.4 - - - +
308A GLN* 1.3 59.4 + - + +
309A LEU 2.9 10.0 + - - -
310A LEU* 3.5 14.1 + - - +
311A PRO* 3.1 19.9 - - - +
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A THR* 3.1 33.9 + - + +
305A PHE* 3.3 13.9 + - + +
307A ASN* 1.3 76.4 - - + +
309A LEU* 1.3 59.0 + - - +
310A LEU 3.8 0.2 - - - -
311A PRO* 4.0 8.7 - - - +
312A LEU* 4.0 14.7 - - - +
373A LYS* 4.0 17.3 + - - +
376A ASP* 4.3 13.2 - - - +
331B ASP* 3.7 42.4 + - - +
332B ARG 5.4 0.8 + - - -
333B GLN* 5.3 2.2 + - - +
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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