Contacts of the helix formed by residues 267 - 275 (chain A) in PDB entry 3QNQ
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 MET 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.5 9.0 - - - -
77A PHE* 4.2 14.4 - - - -
80A MET* 5.7 0.9 - - - +
263A TRP 3.3 9.4 + - - +
264A LEU* 3.0 43.3 - - + +
265A SER 3.1 0.6 - - - -
266A LEU* 1.3 76.0 - - - +
268A ASP* 1.3 63.7 + - - +
270A ASN* 3.8 1.8 - - - -
271A ARG* 3.3 19.6 + - - +
285A THR* 3.6 20.6 - - - -
286A ALA* 4.4 2.5 - - + +
287A GLN* 3.2 33.2 - - - +
377A GLY* 3.3 35.7 - - - +
379A ALA* 3.4 19.3 - - + -
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Residues in contact with ASP 268 (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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77A PHE* 3.8 13.1 - - - +
78A ASN* 4.7 2.1 - - - +
80A MET* 5.0 4.7 - - - -
142A GLY* 4.9 0.7 - - - -
143A SER* 2.6 47.8 + - - +
264A LEU 3.6 3.6 - - - +
265A SER 3.0 5.0 + - - +
267A MET* 1.3 84.7 - - - +
269A GLN* 1.3 51.6 + - - +
270A ASN 3.2 1.1 - - - -
271A ARG* 2.7 48.9 + - - +
272A ILE* 2.7 39.2 + - - +
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Residues in contact with GLN 269 (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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225A SER* 5.6 0.9 + - - -
265A SER* 3.0 25.2 + - - +
266A LEU* 3.3 25.7 - - - +
268A ASP* 1.3 74.0 - - - +
270A ASN* 1.3 60.7 + - - +
272A ILE* 4.0 16.5 - - + +
273A ALA* 4.0 8.1 + - - +
281A PRO* 3.3 22.4 - - + +
282A ASN* 2.7 33.7 + - - +
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Residues in contact with ASN 270 (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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266A LEU 3.1 22.0 + - - +
267A MET* 3.9 7.2 - - - +
268A ASP 3.2 0.2 - - - -
269A GLN* 1.3 77.6 - - - +
271A ARG* 1.3 60.1 + - - +
273A ALA* 3.8 1.0 + - - +
274A PHE 3.1 20.1 + - - -
280A VAL* 3.2 19.5 - - - +
281A PRO* 3.8 7.3 - - - +
282A ASN* 2.9 48.3 + - - +
285A THR* 4.0 7.0 - - + +
374A ARG* 4.2 0.6 - - - +
375A PRO* 2.8 34.7 + - - +
376A SER 3.0 13.3 - - - +
377A GLY* 4.2 2.9 - - - -
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Residues in contact with ARG 271 (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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43A LEU* 4.2 13.2 - - + -
73A VAL* 3.8 13.3 - - - +
77A PHE* 3.5 37.5 - - - +
78A ASN* 2.9 31.9 + - - +
267A MET 3.3 11.9 + - - +
268A ASP* 2.7 35.3 + - - +
270A ASN* 1.3 79.5 - - - +
272A ILE* 1.3 93.6 + - - +
273A ALA 3.2 0.6 + - - -
274A PHE* 3.9 3.1 - - + +
275A GLN* 3.0 53.3 + - + +
376A SER 3.7 6.9 + - - -
377A GLY 4.0 9.9 - - - +
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Residues in contact with ILE 272 (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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78A ASN* 5.1 1.1 - - - +
268A ASP* 2.7 24.1 + - - +
269A GLN* 4.1 16.2 - - + +
270A ASN 3.4 0.2 - - - -
271A ARG* 1.3 106.6 - - - +
273A ALA* 1.3 69.0 + - + +
275A GLN* 4.1 4.5 + - - +
276A ALA* 3.8 14.7 + - - +
127D LYS* 3.8 29.8 - - + +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLN 4.0 2.6 + - - +
270A ASN 3.8 3.3 + - - +
271A ARG 3.2 0.4 - - - -
272A ILE* 1.3 82.5 - - + +
274A PHE* 1.3 56.4 + - - +
276A ALA* 2.6 39.7 + - - -
277A GLY 3.3 0.3 + - - -
278A GLN* 3.5 29.5 + - + +
279A ASP 4.1 4.0 - - - +
280A VAL* 4.2 3.1 - - + -
281A PRO* 3.8 28.9 - - + -
127D LYS* 6.0 1.6 - - - +
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Residues in contact with PHE 274 (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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43A LEU* 4.2 16.6 - - + -
44A ILE* 6.4 0.2 - - + -
47A THR* 3.2 38.8 - - + -
49A PRO* 5.3 1.8 - - + -
270A ASN 3.1 16.9 + - - +
271A ARG* 3.4 5.3 + - - +
273A ALA* 1.3 78.9 - - - +
275A GLN* 1.3 58.6 + - + +
277A GLY* 3.0 19.6 + - - -
278A GLN 4.3 6.2 + - - -
280A VAL* 3.7 13.9 - - + +
376A SER* 3.4 36.3 - - - +
394A SER 4.2 4.9 - - - -
395A GLY* 3.6 31.2 - - - -
397A LYS* 6.2 1.6 - - + -
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Residues in contact with GLN 275 (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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43A LEU* 3.6 31.7 - - + +
46A SER* 5.3 4.7 + - - -
47A THR* 4.6 13.8 - - + +
70A GLY* 5.1 9.4 - - - -
73A VAL* 4.0 7.6 - - - +
271A ARG* 3.0 43.9 + - - +
272A ILE* 4.5 4.5 - - - +
273A ALA 3.0 2.0 + - - -
274A PHE* 1.3 77.1 - - + +
276A ALA* 1.3 56.2 + - - +
277A GLY 3.4 2.0 - - - -
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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