Contacts of the helix formed by residues 318 - 333 (chain A) in PDB entry 3QLE
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 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A PRO* 5.4 1.1 - - - -
317A ASP* 1.3 75.0 - - - +
319A LYS* 1.3 76.2 + - - +
320A LEU 3.3 2.7 - - - -
321A VAL* 3.1 20.0 + - + +
322A ARG* 3.0 58.9 + - + +
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Residues in contact with LYS 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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218A ARG* 3.5 19.3 - - - +
309A MET* 4.2 14.7 - - + +
310A GLU* 5.5 4.8 + - - -
317A ASP* 3.4 31.1 + - - +
318A ASP* 1.3 88.3 + - - +
320A LEU* 1.3 61.7 + - - +
322A ARG* 3.3 10.7 + - + +
323A LEU* 3.2 24.6 + - - +
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Residues in contact with LEU 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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201A PHE* 3.3 49.6 - - + +
202A LEU* 3.8 13.2 - - + -
218A ARG* 3.6 32.4 - - + +
219A PRO 3.7 19.0 + - - +
220A GLY 4.7 2.0 - - - -
221A ALA* 3.7 24.2 - - - -
224A PHE* 3.5 32.5 - - + -
309A MET* 5.5 0.2 - - + -
317A ASP* 4.8 0.2 + - - -
318A ASP 3.3 0.6 - - - -
319A LYS* 1.3 74.4 - - - +
321A VAL* 1.3 67.0 + - - +
323A LEU* 3.2 13.9 + - + +
324A ILE* 3.6 3.2 - - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PRO* 4.9 2.9 - - + +
220A GLY* 4.1 25.4 - - - +
223A TYR* 5.0 15.3 - - + -
318A ASP* 3.1 19.8 + - + +
320A LEU* 1.3 76.0 - - - +
322A ARG* 1.3 65.4 + - + +
324A ILE* 3.2 28.6 + - + +
325A PRO* 3.6 5.2 - - - +
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Residues in contact with ARG 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 ASP* 3.0 49.0 + - - +
319A LYS* 3.8 12.3 - - + +
320A LEU 3.2 0.2 - - - -
321A VAL* 1.3 79.0 - - + +
323A LEU* 1.3 59.3 + - - +
325A PRO* 3.4 14.7 - - - +
326A PHE* 5.1 1.2 + - - +
352A ALA* 3.3 25.4 - - + +
356A ASP* 4.2 12.5 + - - -
1002A 1PE 3.5 34.6 + - - -
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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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201A PHE* 4.0 25.1 - - + -
224A PHE* 4.2 7.4 - - + -
292A ILE* 4.3 9.6 - - + -
307A ILE* 4.6 23.6 - - + -
309A MET* 3.8 30.7 - - + -
319A LYS 3.2 10.5 + - - +
320A LEU* 3.5 10.5 - - + +
321A VAL 3.2 0.6 - - - -
322A ARG* 1.3 76.2 - - - +
324A ILE* 1.3 64.5 + - - +
325A PRO 3.4 0.8 - - - -
326A PHE* 3.5 7.2 + - + +
327A LEU* 3.4 34.3 + - + +
351A LEU* 4.7 12.8 - - + -
352A ALA* 4.3 16.8 - - + +
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Residues in contact with ILE 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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220A GLY 5.7 0.2 - - - +
223A TYR* 3.7 35.7 - - + +
224A PHE* 3.9 25.4 - - + -
227A TYR* 3.7 34.5 - - + -
228A LEU* 4.2 11.9 - - + -
320A LEU 3.6 15.5 - - - +
321A VAL* 3.2 13.7 + - + +
323A LEU* 1.3 78.9 - - - +
325A PRO* 1.3 65.9 - - + +
327A LEU* 3.1 6.5 + - - +
328A GLU* 2.7 32.4 + - - +
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Residues in contact with PRO 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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103A ACT 3.5 32.5 - - + +
321A VAL 3.6 7.2 - - - +
322A ARG* 3.4 16.8 - - - +
323A LEU 3.6 0.2 - - - -
324A ILE* 1.3 95.4 - - + +
326A PHE* 1.3 56.5 + - - +
328A GLU* 3.7 7.9 - - + +
329A TYR* 2.8 30.1 + - - +
355A PHE* 3.9 6.4 - - + -
361A LYS* 5.4 4.9 - - + +
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Residues in contact with PHE 326 (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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307A ILE* 4.2 12.6 - - + -
322A ARG 5.1 0.8 + - - +
323A LEU* 3.5 8.6 + - + +
324A ILE 3.3 0.4 - - - -
325A PRO* 1.3 77.5 - - - +
327A LEU* 1.3 70.1 + - + +
329A TYR* 3.2 5.1 + + - +
330A LEU* 2.9 63.1 + - + +
341A ILE* 4.0 17.9 - - + -
342A LEU* 4.4 11.0 - - + -
345A PHE* 3.8 26.9 - + - -
351A LEU* 3.4 37.9 - - + -
352A ALA* 5.5 2.7 - - - -
355A PHE* 3.7 40.3 - + + -
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Residues in contact with LEU 327 (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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194A LEU* 4.3 14.1 - - + -
224A PHE* 4.0 16.8 - - + -
228A LEU* 3.7 29.4 - - + -
232A TYR* 2.6 47.8 + - + +
290A ILE* 4.8 3.4 - - + -
292A ILE* 4.1 13.9 - - + -
307A ILE* 4.3 15.0 - - + -
323A LEU* 3.4 18.8 + - + +
324A ILE 3.1 6.8 + - - +
326A PHE* 1.3 94.9 - - + +
328A GLU* 1.3 62.8 + - - +
330A LEU* 4.6 4.5 - - + -
331A ALA* 3.3 9.0 + - - +
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Residues in contact with GLU 328 (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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227A TYR* 2.5 36.1 + - + -
228A LEU* 4.5 4.1 - - + +
231A TYR* 4.1 17.5 - - + -
324A ILE* 2.7 27.5 + - + +
325A PRO* 3.7 7.7 - - - +
327A LEU* 1.3 73.6 - - - +
329A TYR* 1.3 56.4 + - - +
331A ALA* 3.2 5.1 + - - +
332A THR* 2.9 50.6 + - + +
361A LYS* 4.6 13.2 + - - -
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Residues in contact with TYR 329 (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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325A PRO 2.8 18.6 + - - +
326A PHE* 3.3 10.5 - + - +
328A GLU* 1.3 76.1 - - - +
330A LEU* 1.3 73.1 + - + +
332A THR* 3.2 7.2 + - - -
333A GLN* 3.1 66.9 + - + +
335A THR* 5.8 0.4 - - - -
341A ILE* 4.8 17.3 - - + -
355A PHE* 3.6 34.5 - + + -
359A VAL* 5.7 3.6 - - + -
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Residues in contact with LEU 330 (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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192A LEU* 4.0 6.3 - - + -
232A TYR* 3.4 20.0 - - - +
290A ILE* 4.1 26.2 - - + -
326A PHE* 2.9 56.0 + - + +
327A LEU* 3.8 3.1 - - + +
328A GLU 3.4 0.2 - - - -
329A TYR* 1.3 77.4 - - + +
331A ALA* 1.3 61.8 + - - +
333A GLN 3.7 1.4 + - - -
335A THR* 2.6 43.2 + - + +
338A VAL* 4.1 22.0 - - + +
341A ILE* 4.3 20.9 - - + -
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Residues in contact with ALA 331 (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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191A PRO* 4.7 7.2 - - + +
192A LEU* 3.9 13.2 - - + -
231A TYR* 3.6 41.8 - - + +
232A TYR* 4.0 7.2 - - + -
327A LEU 3.3 7.9 + - - +
328A GLU 3.2 6.7 + - - +
329A TYR 3.2 0.8 - - - -
330A LEU* 1.3 80.7 - - - +
332A THR* 1.3 60.2 + - - +
334A GLN 3.2 17.9 + - - +
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Residues in contact with THR 332 (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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231A TYR* 3.7 28.7 - - + +
328A GLU* 2.9 34.7 + - + +
329A TYR* 3.4 11.4 + - - -
331A ALA* 1.3 76.5 - - - +
333A GLN* 1.3 69.2 + - - +
334A GLN 3.4 3.6 - - - -
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Residues in contact with GLN 333 (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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329A TYR* 3.1 58.0 + - + +
330A LEU 3.7 0.2 + - - -
331A ALA 3.3 0.2 - - - -
332A THR* 1.3 86.8 + - - +
334A GLN* 1.3 82.7 + - - +
335A THR* 3.8 12.1 + - - +
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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