Contacts of the helix formed by residues 290 - 303 (chain A) in PDB entry 6UQY
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 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER* 3.5 1.8 - - - -
75A ASN* 3.4 13.7 - - - +
264A CYS* 4.8 0.4 - - + -
278A PRO 3.8 12.8 - - - +
281A TYR* 2.7 33.7 + - + +
282A TYR 2.9 8.8 + - - -
283A PHE 3.4 28.0 - - - +
284A TRP* 3.5 12.8 - - + +
289A PRO* 1.3 76.7 - - - +
291A ARG* 1.3 65.2 + - - +
292A ARG* 3.2 12.6 + - - +
293A VAL* 3.2 8.2 + - - +
294A HIS* 3.0 21.0 + - - -
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Residues in contact with ARG 291 (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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74A SER* 3.4 4.3 + - - -
75A ASN* 2.8 44.0 + - - +
76A GLY* 3.6 22.7 - - - -
77A PRO* 4.5 9.2 - - + +
278A PRO* 5.9 4.0 - - - +
279A ASP* 2.9 37.9 + - - +
290A THR* 1.3 72.3 - - - +
292A ARG* 1.3 60.2 + - - +
294A HIS* 3.4 9.1 + - - +
295A GLN* 2.8 28.9 + - - +
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Residues in contact with ARG 292 (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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255A TYR* 3.0 33.7 + - - +
257A LEU* 4.2 11.7 - - + -
279A ASP* 3.6 45.6 + - - +
281A TYR 4.8 1.1 - - - +
290A THR* 3.1 9.4 + - - +
291A ARG* 1.3 82.6 - - - +
293A VAL* 1.3 61.6 + - - +
295A GLN* 3.3 21.7 + - - +
296A LEU* 3.0 59.5 + - + +
299A GLU* 5.1 2.2 + - - -
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Residues in contact with VAL 293 (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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241A HIS* 5.5 3.8 - - + -
244A PHE* 4.0 8.9 - - + -
248A LEU* 4.2 11.7 - - + -
257A LEU* 4.5 7.0 - - + -
281A TYR 4.4 1.1 - - - +
282A TYR* 3.5 66.4 - - + +
289A PRO* 3.7 22.2 - - + -
290A THR* 3.2 10.5 + - - +
292A ARG* 1.3 72.8 - - - +
294A HIS* 1.3 60.4 + - - +
296A LEU* 3.2 8.3 + - - +
297A ALA* 2.8 28.8 + - + +
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Residues in contact with HIS 294 (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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38A SER 4.9 1.4 + - - -
39A TYR* 3.3 35.9 - - + -
73A TRP 5.3 0.8 + - - -
74A SER* 3.7 24.4 - - - -
77A PRO 3.3 24.2 - - - +
78A THR* 3.6 12.5 - - - +
79A ALA* 3.1 30.2 + - + +
82A VAL* 4.1 2.4 - - - +
143A PHE* 5.8 1.3 - + - -
288A ASN* 5.4 0.4 + - - -
289A PRO* 3.7 30.5 + - + +
290A THR 3.0 19.2 + - - -
291A ARG 3.7 4.9 - - - +
293A VAL* 1.3 76.4 - - - +
295A GLN* 1.3 57.5 + - - +
297A ALA* 4.2 4.9 - - - +
298A GLY* 2.9 25.1 + - - -
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Residues in contact with GLN 295 (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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82A VAL* 3.7 16.7 - - + +
85A ARG* 2.5 34.5 + - - +
86A GLN* 4.6 6.5 - - - +
291A ARG 2.8 18.6 + - - +
292A ARG* 3.5 22.2 - - - +
293A VAL 3.2 0.2 - - - -
294A HIS* 1.3 73.3 - - - +
296A LEU* 1.3 60.7 + - - +
299A GLU* 2.5 71.6 + - - +
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Residues in contact with LEU 296 (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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244A PHE* 3.6 15.2 - - + -
248A LEU* 3.8 27.8 - - + -
255A TYR* 4.0 28.7 - - + -
257A LEU* 5.0 2.7 - - + -
292A ARG* 3.0 62.3 + - + +
293A VAL* 3.2 4.5 + - - +
295A GLN* 1.3 75.5 - - - +
297A ALA* 1.3 56.1 + - - +
299A GLU* 3.5 17.3 + - - +
300A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 297 (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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79A ALA* 3.9 13.2 - - + -
239A PHE* 4.2 0.8 - - + -
241A HIS* 4.3 13.9 - - - +
244A PHE* 3.4 26.6 - - + -
293A VAL* 2.8 17.7 + - + +
294A HIS* 3.7 6.7 - - - +
295A GLN 3.2 0.2 - - - -
296A LEU* 1.3 74.3 - - - +
298A GLY* 1.3 61.3 + - - +
300A ALA* 3.2 3.7 + - - +
301A MET* 2.9 39.3 + - + +
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Residues in contact with GLY 298 (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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79A ALA* 3.4 26.7 - - - +
82A VAL* 4.0 11.0 - - - -
83A LEU* 3.9 7.2 - - - -
294A HIS 2.9 14.2 + - - -
295A GLN 3.8 0.9 - - - -
297A ALA* 1.3 72.2 - - - +
299A GLU* 1.3 64.3 + - - +
301A MET* 3.4 7.1 + - - +
302A ALA* 3.0 25.0 + - - +
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Residues in contact with GLU 299 (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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82A VAL* 4.4 0.9 - - + -
86A GLN* 4.2 23.2 + - - +
292A ARG* 5.1 2.4 + - - -
295A GLN* 2.5 55.4 + - - +
296A LEU* 3.8 23.7 - - - +
297A ALA 3.2 0.2 - - - -
298A GLY* 1.3 75.9 - - - +
300A ALA* 1.3 62.4 + - - +
302A ALA* 3.3 8.2 + - - +
303A ALA* 3.2 19.6 + - - +
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Residues in contact with ALA 300 (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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239A PHE* 3.7 25.2 - - + -
244A PHE* 4.0 14.1 - - + -
296A LEU 2.9 18.6 + - - +
297A ALA 3.6 4.5 - - - +
299A GLU* 1.3 74.8 - - - +
301A MET* 1.3 64.4 + - - +
303A ALA* 3.3 19.9 + - - +
304A ARG* 4.5 3.5 + - - +
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Residues in contact with MET 301 (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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79A ALA* 3.9 30.5 - - + +
83A LEU* 3.8 13.0 - - + -
141A PHE* 3.8 25.8 - - + -
143A PHE* 4.3 4.5 - - + -
188A LEU* 4.4 10.6 - - + +
190A VAL* 4.0 15.0 - - + -
239A PHE* 3.9 46.0 - - + -
241A HIS* 4.2 13.5 - - + -
297A ALA* 2.9 20.5 + - + +
298A GLY* 3.7 7.4 - - - +
300A ALA* 1.3 77.6 - - - +
302A ALA* 1.3 62.8 + - - +
303A ALA 3.3 0.7 + - - -
304A ARG* 3.6 10.4 + - - +
305A TYR* 3.7 17.0 - - - -
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Residues in contact with ALA 302 (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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83A LEU* 3.5 17.7 - - + +
86A GLN* 3.8 28.0 - - + +
87A LEU* 3.8 10.9 - - + +
298A GLY 3.0 18.8 + - - +
299A GLU 3.6 6.3 - - - +
300A ALA 3.2 0.2 - - - -
301A MET* 1.3 74.1 - - - +
303A ALA* 1.3 63.1 + - - +
304A ARG 3.0 5.3 + - - -
305A TYR* 3.0 25.5 + - - +
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Residues in contact with ALA 303 (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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25A LEU* 3.4 18.5 - - - +
299A GLU 3.2 10.9 + - - +
300A ALA* 3.3 18.2 - - - +
301A MET 3.2 1.4 - - - -
302A ALA* 1.3 75.9 - - - +
304A ARG* 1.3 61.1 + - + +
305A TYR 3.2 2.3 - - - +
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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