Contacts of the helix formed by residues 270 - 278 (chain A) in PDB entry 3QV2
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 THR 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASP* 2.7 28.9 + - - +
199A VAL* 3.6 31.6 - - + -
203A TYR* 4.0 18.2 - - + -
267A ARG* 4.0 2.0 - - - +
269A PHE* 1.3 76.0 - - - +
271A PRO* 1.3 76.1 - - - +
272A ASN* 3.5 4.2 + - - +
273A GLU* 2.8 35.5 + - - +
274A ILE* 3.1 12.8 + - - +
297A TYR* 3.6 2.9 - - - -
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Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 3.6 13.2 - - + +
270A THR* 1.3 88.7 - - - +
272A ASN* 1.3 55.7 + - - +
274A ILE* 3.3 2.0 + - + -
275A LYS* 2.9 25.5 + - - +
286A THR* 3.9 8.1 - - - +
287A GLN* 5.9 1.6 - - - +
293A ASP* 3.9 18.4 - - + +
296A GLN* 3.4 31.9 - - + +
297A TYR* 3.5 28.0 - - + +
300A LEU* 3.2 24.5 - - + +
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Residues in contact with ASN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP* 3.4 16.1 - - - +
270A THR* 3.2 8.8 + - - +
271A PRO* 1.3 81.4 - - - +
273A GLU* 1.3 57.8 + - - +
275A LYS* 3.4 28.7 - - - +
276A LYS* 3.1 31.9 + - - +
282A SER 5.7 0.2 + - - -
284A PHE 4.7 0.8 + - - -
285A THR* 4.6 14.1 + - - +
286A THR* 5.5 1.5 - - - +
287A GLN* 6.2 0.4 - - - +
326A SO4 3.3 25.0 + - - -
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TYR 3.5 18.8 - - - +
195A LEU* 3.4 6.0 - - - -
196A ASP* 2.8 35.9 + - - +
267A ARG* 2.9 36.1 + - - -
269A PHE* 3.1 22.7 - - + -
270A THR* 2.8 38.1 + - - +
272A ASN* 1.3 75.4 - - - +
274A ILE* 1.3 64.8 + - - +
276A LYS* 3.2 5.3 + - - +
277A ILE* 3.0 30.0 + - + +
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Residues in contact with ILE 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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230A PHE* 3.6 46.0 - - + -
234A TYR* 4.0 5.2 - - + -
269A PHE* 4.4 3.1 - - + -
270A THR 3.1 10.0 + - - +
271A PRO* 3.6 5.8 - - + +
273A GLU* 1.3 75.8 - - - +
275A LYS* 1.3 58.4 + - - +
277A ILE* 3.0 9.4 + - - +
278A HIS* 2.8 57.8 + - + +
297A TYR* 3.7 36.6 - - + +
300A LEU* 4.1 19.1 - - + -
301A GLY 6.1 0.2 - - - +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO 2.9 13.9 + - - +
272A ASN* 3.4 35.4 + - - +
273A GLU 3.2 0.2 - - - -
274A ILE* 1.3 77.3 - - - +
276A LYS* 1.3 74.2 + - - +
278A HIS* 4.8 0.2 - - - -
279A GLY 3.4 3.3 + - - -
280A PHE* 3.2 50.2 + - + +
281A SER 3.3 14.4 + - - +
282A SER* 3.5 14.8 + - - +
284A PHE* 3.0 48.1 + - + +
285A THR* 4.8 1.8 - - - +
286A THR* 4.7 5.6 - - + +
300A LEU* 4.0 16.6 - - + +
326A SO4 5.3 2.4 + - - -
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Residues in contact with LYS 276 (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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193A ASN 5.2 3.2 + - - +
194A TYR* 3.1 53.1 + - + +
195A LEU 3.9 3.4 + - - -
196A ASP* 2.7 31.5 + - - +
272A ASN* 3.1 27.3 + - - +
273A GLU* 3.6 4.7 - - - +
274A ILE 3.2 0.2 - - - -
275A LYS* 1.3 90.5 - - - +
277A ILE* 1.3 65.4 + - - +
279A GLY* 3.1 13.7 + - - +
280A PHE 4.8 5.6 - - - +
282A SER* 5.9 2.5 - - - -
307A PHE* 3.8 2.3 - - - -
326A SO4 3.3 30.6 + - - +
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Residues in contact with ILE 277 (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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161A ILE* 4.0 9.8 - - + +
162A PRO* 4.7 3.8 - - + +
163A ASN* 3.6 36.5 - - + +
191A ILE* 5.8 2.9 - - + -
194A TYR* 3.7 33.4 - - + -
227A THR* 4.3 15.5 - - + +
230A PHE* 3.8 24.5 - - + -
269A PHE* 4.9 11.0 - - + -
273A GLU* 3.0 24.3 + - + +
274A ILE* 3.0 7.8 + - - +
276A LYS* 1.3 75.5 - - - +
278A HIS* 1.3 65.0 + - + +
279A GLY 3.1 0.7 + - - -
305A SER* 5.3 1.0 + - - -
307A PHE* 3.5 15.8 - - - -
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Residues in contact with HIS 278 (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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163A ASN* 4.7 8.2 + - - -
165A ARG* 3.7 31.9 + - - -
230A PHE* 4.3 12.0 - + + -
274A ILE* 2.8 37.3 + - + +
276A LYS 3.2 0.2 - - - -
277A ILE* 1.3 87.9 - - + +
279A GLY* 1.3 56.2 + - - +
280A PHE* 3.5 17.2 - - + -
300A LEU* 3.3 24.2 + - - +
303A SER* 2.8 19.6 + - - -
304A VAL 3.3 15.8 + - - +
305A SER* 4.6 5.6 - - - +
306A CYS* 2.8 35.4 + - - +
307A PHE* 3.9 3.3 + - - -
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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