Contacts of the helix formed by residues 308 - 322 (chain A) in PDB entry 1YHV
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 LYS 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLN* 5.1 3.7 - - - +
307A PRO* 1.4 96.1 - - + +
309A LYS* 1.3 65.4 + - - +
310A GLU* 3.1 3.8 - - + -
311A LEU* 3.0 46.0 + - + +
312A ILE* 3.6 3.3 + - - +
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Residues in contact with LYS 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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250A ASP* 4.4 19.7 - - - +
253A ILE* 3.8 44.1 - - + +
254A LEU* 6.2 0.7 - - - -
303A LEU* 3.4 54.1 - - + +
304A GLN* 4.3 4.7 - - - +
306A GLN* 3.4 25.0 + - + +
307A PRO 3.7 3.2 + - - +
308A LYS* 1.3 71.6 - - - +
310A GLU* 1.3 60.5 + - - +
311A LEU 3.2 0.2 - - - -
312A ILE* 2.4 37.2 - - + +
313A ILE* 3.1 8.3 + - - +
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Residues in contact with GLU 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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249A SER 5.9 0.5 + - - -
252A GLU* 4.8 8.3 - - - +
253A ILE* 3.9 28.6 - - + +
308A LYS* 3.1 2.9 + - + -
309A LYS* 1.3 78.7 - - - +
311A LEU* 1.3 59.6 + - + +
313A ILE* 3.7 19.2 - - - +
314A ASN* 2.9 29.3 + - - +
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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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308A LYS* 3.0 38.3 + - + +
310A GLU* 1.3 81.2 - - + +
312A ILE* 1.3 57.3 + - - +
314A ASN* 3.4 12.2 + - + +
315A GLU* 2.8 30.1 + - - +
409A GLY* 3.5 30.1 - - - +
410A PHE* 4.5 17.9 - - + -
411A CYS 6.2 0.7 - - - +
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Residues in contact with ILE 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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257A LEU* 5.0 4.9 - - + -
299A ARG* 5.0 3.4 - - - +
301A MET* 3.2 35.0 - - + -
303A LEU* 4.9 5.8 - - + -
306A GLN* 5.2 5.8 - - + -
308A LYS 3.6 2.5 + - - +
309A LYS* 2.4 46.0 - - + +
311A LEU* 1.3 76.9 - - - +
313A ILE* 1.3 74.7 + - + +
315A GLU* 3.2 13.3 + - - +
316A ILE* 3.0 31.2 + - + +
340A LEU* 3.0 39.7 - - + -
342A VAL* 5.1 1.3 - - + -
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Residues in contact with ILE 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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253A ILE* 4.0 22.7 - - + +
256A LYS* 3.5 35.2 - - + -
257A LEU* 3.8 25.6 - - + -
260A ILE* 4.0 10.9 - - + +
309A LYS 3.1 9.8 + - - +
310A GLU* 3.7 27.1 - - - +
312A ILE* 1.3 84.4 - - - +
314A ASN* 1.3 63.3 + - - +
316A ILE* 3.2 6.5 + - - +
317A LEU* 3.0 42.2 + - + +
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Residues in contact with ASN 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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310A GLU 2.9 18.2 + - - +
311A LEU* 3.6 13.1 - - + +
313A ILE* 1.3 79.3 - - - +
315A GLU* 1.3 64.0 + - - +
317A LEU* 3.3 7.3 + - - +
318A VAL* 2.9 38.2 + - - +
408A PHE 4.3 2.4 - - - +
409A GLY 5.6 1.0 - - - +
411A CYS* 3.5 31.3 + - - +
413A GLN* 3.7 14.8 + - - +
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Residues in contact with GLU 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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299A ARG* 3.4 35.6 + - - -
311A LEU 2.8 18.7 + - - +
312A ILE* 3.2 12.1 + - - +
314A ASN* 1.3 77.7 - - - +
316A ILE* 1.3 63.4 + - + +
318A VAL* 3.9 1.5 - - - +
319A MET* 3.0 50.3 + - + +
407A ASP* 4.2 8.1 - - - +
408A PHE* 3.5 40.2 + - + +
409A GLY* 3.8 17.9 + - - +
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Residues in contact with ILE 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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257A LEU* 5.6 6.1 - - + -
260A ILE* 3.7 25.8 - - + -
299A ARG* 6.2 0.2 - - - +
312A ILE* 3.0 19.9 + - + +
313A ILE* 3.2 8.0 + - - +
315A GLU* 1.3 76.8 - - + +
317A LEU* 1.3 60.9 + - + +
319A MET* 3.3 9.5 + - + +
320A ARG* 2.9 31.3 + - + +
330A TYR* 3.4 48.3 - - + +
333A SER* 4.6 4.3 - - - +
340A LEU* 5.9 0.9 - - + -
342A VAL* 3.6 32.8 - - + -
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Residues in contact with LEU 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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256A LYS* 4.3 16.8 - - - +
260A ILE* 3.8 22.9 - - + -
313A ILE* 3.0 36.4 + - + +
314A ASN* 3.9 7.0 - - - +
316A ILE* 1.3 77.4 - - - +
318A VAL* 1.3 62.6 + - + +
320A ARG* 3.6 38.8 + - - +
321A GLU* 3.3 28.8 + - + +
413A GLN* 6.1 0.4 - - - +
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Residues in contact with VAL 318 (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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314A ASN* 2.9 29.5 + - - +
315A GLU 4.0 2.9 - - - +
317A LEU* 1.3 74.3 - - + +
319A MET* 1.3 67.1 + - - +
321A GLU 3.4 0.5 + - - -
322A ASN* 2.9 46.3 + - + +
385A VAL* 4.3 11.9 - - + -
408A PHE* 4.1 17.0 - - + -
411A CYS* 3.9 26.9 - - - -
413A GLN* 3.5 33.7 - - + +
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Residues in contact with MET 319 (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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299A ARG* 5.5 1.3 - - - +
315A GLU* 3.0 46.6 + - + +
316A ILE* 3.9 12.1 - - + +
318A VAL* 1.3 78.6 - - - +
320A ARG* 1.3 62.9 + - - +
321A GLU 3.3 0.7 + - - -
322A ASN* 3.4 14.2 + - - +
323A LYS* 3.6 19.1 - - - +
327A ILE* 5.8 3.8 - - + -
328A VAL 5.0 4.0 - - - +
330A TYR* 3.8 26.0 - - + +
342A VAL* 4.6 2.2 - - + -
344A MET* 3.6 41.3 - - - -
406A THR* 5.8 0.2 - - - -
407A ASP 5.8 1.6 - - - -
408A PHE* 4.0 32.3 - - + -
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Residues in contact with ARG 320 (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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260A ILE* 4.4 23.5 + - - +
316A ILE* 2.9 20.6 + - + +
317A LEU* 3.6 32.6 - - - +
318A VAL 3.3 0.2 - - - -
319A MET* 1.3 78.7 - - - +
321A GLU* 1.3 89.1 + - - +
322A ASN 3.7 0.2 + - - -
323A LYS* 3.9 17.3 + - - +
330A TYR* 4.1 27.5 - - + -
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Residues in contact with GLU 321 (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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317A LEU* 3.3 18.4 + - + +
319A MET 3.3 0.4 - - - -
320A ARG* 1.3 113.9 + - - +
322A ASN* 1.3 72.3 + - - +
323A LYS 3.8 1.8 - - - -
379A PHE* 5.2 0.9 - - - -
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Residues in contact with ASN 322 (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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318A VAL* 2.9 43.2 + - + +
319A MET* 3.4 7.4 + - - +
321A GLU* 1.3 89.8 + - - +
323A LYS* 1.3 65.5 + - - +
327A ILE* 3.5 15.8 - - + +
379A PHE* 3.4 24.6 - - + -
380A LEU* 4.4 9.8 - - + +
383A ASN* 3.7 27.9 + - - +
385A VAL* 4.0 15.7 - - - +
408A PHE* 6.3 0.2 - - + -
413A GLN* 5.1 4.2 - - - +
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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