Contacts of the helix formed by residues 310 - 325 (chain A) in PDB entry 1YQL
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 TYR 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 4.2 29.7 - - + +
109A LEU* 3.9 30.1 - - + -
113A TRP* 3.3 23.6 - - + +
262A PRO* 3.2 34.5 - - + +
307A TRP 4.8 1.0 + - - -
308A GLY 3.2 1.4 - - - -
309A PRO* 1.3 91.2 - - + +
311A ALA* 1.3 64.4 + - - +
312A GLY 3.1 2.7 - - - -
313A TRP* 2.9 27.5 + + + +
314A ALA 3.2 8.8 + - - -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO 3.4 0.4 + - - -
263A GLN 4.1 3.8 - - - +
265A VAL* 3.6 21.8 - - + -
303A PHE 3.9 8.1 - - - +
304A ARG* 3.7 17.7 - - - -
307A TRP* 3.5 21.0 - - + -
308A GLY 3.1 17.9 + - - +
309A PRO 3.3 2.0 + - - -
310A TYR* 1.3 74.9 - - - +
312A GLY* 1.3 61.0 + - - +
314A ALA 3.2 1.1 + - - +
315A GLN* 2.8 29.6 + - - +
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.7 15.1 - - - +
262A PRO 2.9 12.7 + - - -
263A GLN 4.0 0.4 - - - -
264A ALA 3.1 28.1 + - - -
265A VAL* 3.9 1.2 - - - +
311A ALA* 1.3 77.1 - - - +
313A TRP* 1.3 60.0 + - - +
315A GLN* 3.0 27.7 - - - +
316A ALA* 3.1 6.4 + - - +
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Residues in contact with TRP 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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101A GLN* 3.8 25.6 - - + -
104A VAL* 3.7 36.1 - - + -
106A LEU* 4.3 6.1 - - + -
109A LEU* 3.7 14.4 - - + -
113A TRP* 3.4 15.7 - + + -
130A VAL 5.2 1.7 - - - +
131A ARG* 3.9 20.4 - - + -
132A LEU* 3.7 56.2 - - + +
256A LEU* 3.9 12.8 + - + +
262A PRO* 3.6 34.9 - - + +
310A TYR* 2.9 22.7 + + - +
312A GLY* 1.3 74.0 - - - +
314A ALA* 1.3 67.3 + - - +
315A GLN 3.0 1.3 - - - -
316A ALA* 2.9 17.7 + - - +
317A VAL* 3.3 9.9 + - - +
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Residues in contact with ALA 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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113A TRP* 3.4 37.5 - - + +
120A PHE* 3.9 10.0 - - + -
307A TRP* 3.4 40.2 - - + -
310A TYR 3.2 2.8 + - - +
311A ALA 3.2 3.0 + - - +
313A TRP* 1.3 78.1 - - - +
315A GLN* 1.3 62.4 + - - +
317A VAL* 3.1 14.8 + - - +
318A LEU* 3.4 12.3 + - - +
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Residues in contact with GLN 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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256A LEU* 3.5 15.4 - - - +
265A VAL* 4.0 20.9 - - + -
266A PRO* 3.7 13.1 - - + +
271A MET* 3.9 18.2 - - + +
307A TRP* 3.7 17.2 - - + -
311A ALA 2.8 13.5 + - - +
312A GLY* 3.0 22.3 - - - +
314A ALA* 1.3 76.6 - - - +
316A ALA* 1.3 62.6 + - - +
317A VAL 3.4 0.2 + - - -
318A LEU* 3.4 2.6 + - - +
319A PHE* 2.9 48.6 + - - +
23C PPW 2.9 41.4 + - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 4.6 9.0 - - + +
130A VAL* 3.8 12.3 - - + -
132A LEU* 3.5 28.9 - - + -
312A GLY 3.1 6.3 + - - +
313A TRP 2.9 11.9 + - - +
315A GLN* 1.3 83.7 + - - +
317A VAL* 1.3 64.0 + - - +
319A PHE* 3.9 4.4 - - - +
320A SER* 2.8 31.5 + - - +
23C PPW 5.8 2.0 - - - +
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Residues in contact with VAL 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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110A TYR* 3.4 42.4 - - + +
113A TRP* 4.2 3.8 - - + -
120A PHE* 3.8 24.9 - - + -
123A VAL* 5.2 1.1 - - + -
124A ALA* 5.0 5.4 - - - -
127A PHE* 3.8 19.0 - - + +
130A VAL* 3.8 18.6 - - + +
313A TRP 3.7 12.1 - - - +
314A ALA 3.1 6.8 + - - +
316A ALA* 1.3 77.2 - - - +
318A LEU* 1.3 63.4 + - + +
320A SER* 3.5 2.3 + - - -
321A ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 4.3 8.3 - - + +
120A PHE* 4.3 18.2 - - + -
123A VAL* 3.6 39.7 - - + -
271A MET* 4.9 2.2 - - + -
274A ILE* 3.8 31.3 - - + +
279A TYR* 3.7 13.7 - - - +
307A TRP* 3.7 29.6 - - + -
314A ALA 3.4 11.0 + - - +
315A GLN 4.1 4.5 - - - +
316A ALA 3.3 0.2 - - - -
317A VAL* 1.3 76.8 - - + +
319A PHE* 1.3 55.6 + - - +
321A ALA* 3.2 3.4 + - - +
322A ASP* 2.7 37.1 + - - +
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Residues in contact with PHE 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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41A SER 3.5 24.7 - - - -
152A ILE* 4.7 2.5 - - + -
268A ASP* 3.5 22.4 - - - -
270A HIS* 3.5 31.4 - + + -
271A MET* 4.2 3.6 - - - -
274A ILE* 4.2 6.1 - - - +
315A GLN* 2.9 30.7 + - - +
316A ALA* 3.9 4.5 - - - +
318A LEU* 1.3 75.7 - - - +
320A SER* 1.3 66.0 + - - +
322A ASP* 3.2 7.2 + - - +
323A LEU* 3.0 39.1 + - + +
23C PPW 3.3 60.8 - + - -
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.7 20.5 + - - -
41A SER* 3.8 13.3 + - - -
43A GLN* 5.4 1.6 + - - -
127A PHE* 4.8 2.7 - - - -
130A VAL* 3.7 19.7 - - - +
316A ALA* 2.8 23.7 + - - +
317A VAL 3.7 3.6 - - - -
319A PHE* 1.3 81.6 - - - +
321A ALA* 1.3 62.1 - - - +
323A LEU* 2.9 25.8 + - - +
324A ARG* 3.2 15.8 + - - +
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Residues in contact with ALA 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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123A VAL* 3.9 20.6 - - + -
127A PHE* 3.3 40.9 - - + -
317A VAL 3.0 18.2 + - - +
318A LEU* 3.2 4.2 + - - +
320A SER* 1.3 76.4 - - - +
322A ASP* 1.3 60.9 + - - +
323A LEU 3.2 1.0 + - - -
324A ARG* 3.4 12.0 + - - +
325A GLN* 3.5 11.8 + - - +
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Residues in contact with ASP 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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270A HIS* 2.6 41.3 + - - +
273A HIS* 4.1 13.7 - - - +
274A ILE* 3.9 19.7 - - + +
277A ARG* 4.0 25.2 + - - +
318A LEU 2.7 21.5 + - - +
319A PHE* 3.5 6.5 - - - +
321A ALA* 1.3 72.7 - - - +
323A LEU* 1.3 62.2 + - - +
325A GLN* 3.9 18.9 - - - +
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Residues in contact with LEU 323 (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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40A PRO 5.1 0.7 - - - +
41A SER* 3.6 26.9 - - - +
152A ILE* 3.4 33.2 - - + -
270A HIS* 3.7 30.1 - - + +
319A PHE* 3.0 26.9 + - + +
320A SER* 2.9 9.9 + - - +
322A ASP* 1.3 75.4 - - - +
324A ARG* 1.3 80.0 + - - +
325A GLN 3.1 8.1 + - - -
23C PPW 4.2 7.9 - - - +
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Residues in contact with ARG 324 (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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36A ASP 3.5 21.9 + - - -
37A LEU* 4.4 17.7 - - + +
40A PRO* 4.1 18.8 + - - +
41A SER* 3.2 27.3 + - - +
127A PHE* 3.3 35.0 - - + -
320A SER* 3.7 9.1 + - - +
321A ALA 3.6 5.4 - - - +
323A LEU* 1.3 86.9 - - - +
325A GLN* 1.3 67.9 + - - +
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Residues in contact with GLN 325 (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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277A ARG* 6.3 0.9 - - - +
321A ALA 3.5 8.5 + - - +
322A ASP* 3.9 20.4 - - - +
323A LEU 3.1 8.2 + - - -
324A ARG* 1.3 85.8 - - - +
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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