Contacts of the helix formed by residues 307 - 317 (chain A) in PDB entry 4YCV
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 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A THR* 4.5 6.5 - - - -
304A ARG* 3.4 28.0 - - - +
306A ALA* 1.3 76.7 - - - +
308A GLU* 1.3 64.1 + - - +
309A LEU 3.6 1.3 - - - -
310A PRO* 3.3 14.6 - - - +
311A LEU* 3.1 21.0 - - - +
324A GLU* 3.3 32.8 - - + +
326A GLY 5.7 1.3 - - - +
328A VAL* 4.7 2.7 - - + -
344A SER* 4.6 13.5 - - - +
346A GLU* 3.2 31.3 + - - +
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Residues in contact with GLU 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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306A ALA* 3.4 19.8 + - + +
307A THR* 1.3 76.5 - - - +
309A LEU* 1.3 87.3 + - + +
311A LEU* 3.1 5.7 + - - +
312A LYS* 2.9 30.2 + - - +
346A GLU* 3.3 11.1 + - - +
348A TYR* 3.0 27.3 + - + +
478A LEU* 3.7 23.5 - - - +
505A TYR* 4.0 11.1 + - - -
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Residues in contact with LEU 309 (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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308A GLU* 1.3 90.3 - - + +
310A PRO* 1.3 66.0 - - + +
312A LYS* 3.2 32.8 + - - +
313A MET* 2.9 33.8 + - - +
478A LEU* 5.7 1.6 - - + -
535A LEU 5.2 2.5 - - - +
536A ASP* 4.1 32.1 - - + +
539A PHE* 4.0 26.9 - - + -
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Residues in contact with PRO 310 (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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275A THR* 3.4 28.9 - - + +
276A PRO* 4.8 2.5 - - + -
279A ASN* 5.6 8.3 - - - +
306A ALA 5.4 1.8 - - - +
307A THR* 3.3 17.3 - - - +
309A LEU* 1.3 95.9 - - + +
311A LEU* 1.3 55.2 + - - +
313A MET* 3.3 14.5 + - + +
314A LEU* 2.9 32.3 + - - +
576B PHE* 3.6 28.7 - - + -
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Residues in contact with LEU 311 (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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273A VAL* 3.6 31.2 - - + -
275A THR* 3.9 10.8 - - - +
307A THR* 3.1 39.7 - - - +
308A GLU 3.1 7.3 + - - +
310A PRO* 1.3 74.9 - - - +
312A LYS* 1.3 62.0 + - - +
314A LEU* 3.0 11.5 + - + +
315A ILE* 2.9 28.8 + - - +
322A VAL* 3.8 12.6 - - + +
323A TYR* 4.7 1.3 - - - -
324A GLU* 4.0 10.5 - - + +
346A GLU 3.3 25.1 - - - +
347A PHE* 4.8 0.7 - - - -
348A TYR* 3.7 22.0 - - + -
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Residues in contact with LYS 312 (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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308A GLU* 2.9 35.9 + - - +
309A LEU* 3.3 29.9 - - - +
311A LEU* 1.3 75.3 - - - +
313A MET* 1.3 58.0 + - - +
315A ILE* 2.9 26.4 + - + +
316A VAL* 3.0 19.1 + - - +
348A TYR* 3.5 25.6 - - + -
478A LEU* 4.2 10.7 - - - +
505A TYR* 4.6 0.6 + - - -
507A GLU* 3.1 47.5 + - + +
539A PHE* 3.5 27.9 - - + -
547A LEU* 3.7 8.7 - - + +
550A THR* 5.8 0.7 - - - +
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Residues in contact with MET 313 (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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309A LEU* 2.9 18.8 + - - +
310A PRO* 3.4 17.3 - - + +
311A LEU 3.2 0.2 - - - -
312A LYS* 1.3 75.6 - - - +
314A LEU* 1.3 58.6 + - - +
316A VAL* 3.3 12.9 + - - +
317A GLY* 3.1 20.1 + - - -
535A LEU 4.9 2.5 - - - +
538A ALA* 4.0 25.1 - - + +
539A PHE* 3.9 24.0 - - + -
542A SER* 3.4 19.7 - - - +
235B ARG 4.5 8.1 - - - +
237B ARG 5.0 0.4 - - - +
238B TYR* 3.5 30.1 - - + +
576B PHE* 3.6 27.6 - - + -
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Residues in contact with LEU 314 (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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273A VAL* 3.6 42.6 - - + -
275A THR* 4.9 2.5 - - - +
310A PRO 2.9 18.1 + - - +
311A LEU* 3.0 16.4 + - + +
313A MET* 1.3 74.1 - - - +
315A ILE* 1.3 64.2 + - - +
317A GLY* 3.0 12.0 + - - +
318A GLY 3.5 0.3 + - - -
319A ILE* 3.2 29.3 + - + +
322A VAL* 4.0 11.9 - - + -
237B ARG* 4.8 2.5 - - + -
238B TYR* 6.3 0.4 - - - +
241B LEU* 4.1 21.1 - - + -
575B LEU* 4.1 19.1 - - + -
576B PHE* 3.8 25.1 - - + -
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Residues in contact with ILE 315 (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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311A LEU 2.9 18.9 + - - +
312A LYS* 2.9 11.9 + - - +
314A LEU* 1.3 77.4 - - - +
316A VAL* 1.3 61.8 + - - +
317A GLY 3.2 0.7 + - - -
318A GLY* 3.3 8.8 + - - -
319A ILE 3.1 25.1 - - - +
320A ASP* 3.5 27.3 - - - +
322A VAL* 3.6 7.0 - - + -
348A TYR* 3.4 43.7 - - + +
349A TRP 4.3 0.7 - - - +
350A ALA* 4.6 1.3 - - + +
547A LEU* 3.5 20.2 - - + -
548A PRO* 3.9 12.7 - - + +
550A THR* 3.6 19.5 - - + +
138B ARG* 5.6 0.2 + - - -
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Residues in contact with VAL 316 (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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312A LYS 3.0 15.0 + - - +
313A MET* 3.4 13.7 - - - +
314A LEU 3.2 0.2 - - - -
315A ILE* 1.3 77.1 - - - +
317A GLY* 1.3 60.0 + - - +
318A GLY 3.2 1.4 + - - -
539A PHE* 6.3 0.9 - - + -
542A SER* 3.6 29.8 - - - +
543A LEU* 5.8 0.7 - - + -
545A TYR* 4.2 9.0 - - + +
547A LEU* 3.8 26.9 - - + +
548A PRO* 4.8 3.4 - - - -
138B ARG* 3.7 27.2 + - - +
238B TYR* 3.9 24.2 - - + -
242B LEU* 3.8 12.6 - - + +
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Residues in contact with GLY 317 (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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313A MET 3.1 6.8 + - - -
314A LEU 3.0 9.5 + - - -
316A VAL* 1.3 77.5 - - - +
318A GLY* 1.3 56.7 + - - +
319A ILE* 3.5 2.8 - - - +
238B TYR* 3.5 27.4 - - - -
241B LEU* 3.1 37.6 - - - +
242B LEU* 3.6 7.5 + - - +
248B ARG* 5.8 1.4 - - - -
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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