Contacts of the helix formed by residues 308 - 318 (chain A) in PDB entry 4LQL
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 ASP 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A VAL 4.8 0.9 - - - +
191A THR* 3.5 29.3 - - + +
276A THR* 3.1 10.7 - - - +
304A GLY* 3.5 15.2 - - - -
305A PRO 3.4 3.5 + - - -
306A GLU 3.1 2.2 - - - -
307A GLY* 1.3 72.5 - - - +
309A PHE* 1.3 60.2 + - - +
310A LYS* 3.5 13.2 + - - +
311A MET* 3.2 20.8 + - - +
312A ALA 3.0 20.3 + - - -
446A HIS* 5.6 0.2 - - - -
447A HIS* 2.1 50.7 + - + +
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Residues in contact with PHE 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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178A ILE* 4.6 7.6 - - + +
180A ARG* 3.6 23.1 - - - +
191A THR 4.4 7.9 + - - +
195A LYS* 5.2 7.2 - - + +
206A VAL* 3.4 43.3 - - + -
276A THR* 4.1 1.8 - - - -
307A GLY 2.8 6.0 + - - +
308A ASP* 1.3 70.2 + - - +
310A LYS* 1.3 67.7 + - - +
312A ALA* 3.4 16.9 - - - +
313A GLY* 3.5 4.7 + - - -
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Residues in contact with LYS 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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189A ALA 4.4 0.4 + - - -
190A VAL* 2.9 24.7 + - - +
191A THR 3.8 5.9 + - - +
192A GLU 2.1 33.2 + - - -
193A GLY* 3.4 15.8 - - - -
308A ASP* 3.3 8.2 + - - +
309A PHE* 1.3 80.2 - - - +
311A MET* 1.3 58.5 + - + +
313A GLY* 4.0 0.9 - - - -
314A LEU* 3.2 26.0 + - - +
392A THR* 6.0 0.7 - - - +
393A LEU* 3.9 38.8 - - + +
394A SER* 4.0 2.2 - - - +
395A TYR* 3.4 20.6 - - - +
400A TYR* 3.7 26.9 - - + +
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Residues in contact with MET 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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303A PHE 4.6 2.5 - - - +
304A GLY* 4.0 12.1 - - - -
308A ASP* 3.2 18.5 + - - +
310A LYS* 1.3 77.9 - - + +
312A ALA* 1.3 56.4 - - - +
314A LEU* 4.1 6.7 - - + +
315A THR* 2.2 41.2 + - - -
329A LEU* 5.2 6.7 - - + -
392A THR* 4.9 6.1 - - - +
447A HIS* 4.0 23.6 - - + +
448A THR* 3.5 26.0 - - - +
449A VAL* 4.4 10.3 - - + -
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Residues in contact with ALA 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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178A ILE* 3.7 20.6 - - + -
274A ALA* 4.1 5.2 - - - -
275A PHE 4.0 6.3 - - - +
276A THR* 3.7 17.7 - - + -
302A GLY* 3.5 6.6 - - - -
303A PHE 4.0 0.2 - - - -
304A GLY* 3.6 14.5 - - - +
308A ASP 3.0 15.8 + - - +
309A PHE* 3.4 12.1 - - - +
311A MET* 1.3 71.5 - - - +
313A GLY* 1.3 58.4 + - - +
315A THR* 2.5 21.0 + - - -
316A ARG* 3.2 10.9 + - - +
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Residues in contact with GLY 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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176A ILE* 5.6 2.9 - - - -
178A ILE* 5.0 5.0 - - - +
204A TRP* 4.6 17.4 - - - -
274A ALA* 4.7 2.7 - - - +
309A PHE 3.5 6.9 + - - -
310A LYS 4.0 2.2 - - - -
312A ALA* 1.3 80.1 - - - +
314A LEU* 1.3 57.2 + - - +
315A THR 3.6 0.2 - - - -
316A ARG* 3.4 10.3 - - - +
317A LEU* 2.9 34.5 + - - +
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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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310A LYS 3.2 18.9 + - - +
311A MET* 3.2 9.6 + - + +
313A GLY* 1.3 72.0 - - - +
315A THR* 1.3 62.8 + - - +
316A ARG 3.2 0.9 - - - -
317A LEU* 4.3 5.6 - - + +
318A LEU* 3.1 42.7 + - + +
391A ILE* 4.0 3.6 - - + +
392A THR* 3.9 33.9 - - - +
393A LEU* 4.5 20.0 - - + +
449A VAL* 3.7 24.8 - - + +
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Residues in contact with THR 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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302A GLY* 4.2 2.7 - - - -
303A PHE 3.3 24.2 + - - -
311A MET* 2.2 29.2 + - - -
312A ALA 2.5 15.1 + - - -
314A LEU* 1.3 72.6 - - - +
316A ARG* 1.3 66.4 + - - +
318A LEU* 3.9 1.5 + - - +
319A LYS* 3.0 29.4 + - - +
327A THR* 5.4 1.1 - - - +
328A ALA 5.9 0.2 - - - -
329A LEU* 4.3 15.5 - - - +
449A VAL* 3.8 19.5 - - - +
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Residues in contact with ARG 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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3A LYS* 5.5 6.3 - - - +
172A GLU* 5.5 5.3 + - - +
176A ILE* 3.5 29.2 - - + +
273A ASP* 3.7 41.7 + - + +
274A ALA* 4.1 6.1 - - + -
300A GLY 3.6 20.1 + - - -
301A TYR* 4.7 2.4 - - - +
302A GLY* 3.5 14.3 - - - +
312A ALA 3.2 14.1 + - - +
313A GLY* 3.4 9.2 - - - +
315A THR* 1.3 87.7 + - - +
317A LEU* 1.3 56.5 + - - +
319A LYS* 2.8 29.2 + - - +
320A ILE* 3.4 26.9 + - - +
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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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169A ALA* 5.0 8.2 - - + +
172A GLU 5.3 0.7 - - - +
173A SER* 3.5 34.5 - - - +
176A ILE* 4.0 16.4 - - + -
204A TRP* 4.2 6.7 - - + -
313A GLY 2.9 24.1 + - - +
314A LEU* 3.5 7.8 + - + +
316A ARG* 1.3 74.5 - - - +
318A LEU* 1.3 58.8 + - + +
319A LYS 3.2 0.4 - - - -
320A ILE* 3.3 24.9 + - - +
321A ALA* 3.5 8.0 + - - +
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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
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314A LEU* 3.1 32.3 + - + +
315A THR 4.8 0.7 - - - +
316A ARG 3.0 0.6 + - - -
317A LEU* 1.3 74.4 - - + +
319A LYS* 1.3 62.1 + - - +
320A ILE 3.3 0.2 - - - -
321A ALA* 3.6 14.7 + - + +
322A ALA* 3.7 8.0 + - - +
327A THR* 3.5 32.1 + - + -
449A VAL* 4.6 9.2 - - + -
454A LEU* 4.2 14.4 - - + +
459A LEU* 5.7 8.3 - - + -
462A LEU* 6.3 3.4 - - + -
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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