Contacts of the helix formed by residues 277 - 285 (chain B) in PDB entry 6CQX
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 PRO 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG* 3.4 20.0 - - - +
264A GLY 3.6 19.5 - - - +
265A ASN* 5.5 1.8 - - - -
266A ASP* 3.6 30.7 - - + +
46B ARG* 4.7 0.4 - - - +
275B THR 3.7 6.7 - - - +
276B ARG* 1.3 89.6 - - + +
278B ALA* 1.3 66.2 + - - +
279B GLN* 4.4 5.8 - - + +
280B VAL* 3.1 28.8 + - + +
281B LEU* 3.7 4.2 + - - +
1D NAG 5.9 3.1 - - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ARG* 3.6 15.6 - - - +
70B TYR* 3.6 33.0 - - + -
94B GLU* 3.8 6.5 + - - +
156B PHE* 3.3 37.9 - - + -
276B ARG 3.5 1.2 + - - -
277B PRO* 1.3 74.6 - - - +
279B GLN* 1.3 61.6 + - - +
281B LEU* 3.3 10.9 + - - +
282B VAL* 3.3 6.8 + - - +
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLY* 6.0 3.1 - - - +
70B TYR* 3.6 27.1 + - + +
71B GLN 5.3 1.4 + - - -
92B LEU* 4.2 10.8 - - - +
277B PRO* 3.2 5.0 - - + +
278B ALA* 1.3 80.5 - - - +
280B VAL* 1.3 56.3 + - + +
282B VAL* 3.3 18.9 + - - +
283B ASN* 3.0 64.1 + - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO 4.2 8.7 - - - +
163A GLY* 6.0 0.4 - - - -
245A ARG* 3.6 48.9 - - - +
266A ASP* 5.0 0.2 - - - +
255B VAL* 3.8 23.3 - - + +
276B ARG* 4.7 5.6 - - + -
277B PRO* 3.1 24.0 + - + +
279B GLN* 1.3 75.4 - - + +
281B LEU* 1.3 64.9 + - - +
283B ASN* 3.3 13.4 + - - +
284B HIS* 3.2 28.1 + - + +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ARG* 4.2 11.2 - - - +
47B PHE* 4.1 26.2 - - + -
155B ALA* 4.6 13.5 - - + +
156B PHE* 4.1 25.6 - - + -
251B LEU* 3.8 21.0 - - + +
255B VAL* 4.2 14.8 - - + -
273B LEU* 4.2 21.1 - - + +
276B ARG* 4.0 21.8 - - + -
277B PRO 3.7 8.5 + - - +
278B ALA 3.3 6.3 + - - +
280B VAL* 1.3 75.1 - - - +
282B VAL* 1.3 63.2 + - - +
283B ASN 3.3 0.2 + - - -
284B HIS 3.3 1.7 + - - -
285B GLU* 3.2 21.5 + - - +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 4.3 7.4 - - + -
71B GLN* 3.8 22.2 - - - +
72B TYR* 3.6 38.6 - - + +
156B PHE* 3.8 20.0 - - + -
278B ALA 3.3 12.0 + - - +
279B GLN* 3.3 25.3 + - - +
280B VAL 3.2 0.2 - - - -
281B LEU* 1.3 79.2 - - - +
283B ASN* 1.3 60.5 + - - +
284B HIS 3.3 0.9 + - - -
285B GLU* 3.3 24.8 + - - +
286B TRP 4.9 0.2 + - - -
296B ARG* 4.6 3.1 + - - -
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Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO 5.1 2.2 + - - -
163A GLY* 4.6 9.9 - - - -
241A MET* 6.0 1.2 - - - +
606A 7PE 3.4 48.1 - - - +
72B TYR* 6.3 0.7 - - - -
279B GLN* 3.0 52.2 + - - +
280B VAL* 3.7 9.8 - - - +
281B LEU 3.2 0.6 - - - -
282B VAL* 1.3 77.4 - - - +
284B HIS* 1.3 71.0 + - + +
286B TRP* 5.2 1.1 + - - +
287B HIS* 4.1 12.6 + - - -
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Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO* 6.1 1.6 - - + -
241A MET* 3.7 43.8 - - + +
242A GLY* 4.7 2.0 + - - -
606A 7PE 6.0 0.2 - - - -
251B LEU* 3.7 22.0 - - + +
254B LEU* 3.7 45.6 + - + +
255B VAL* 3.7 12.3 - - + +
280B VAL* 3.2 27.1 + - + +
281B LEU 3.3 2.0 + - - -
282B VAL 3.2 0.4 - - - -
283B ASN* 1.3 87.4 - - + +
285B GLU* 1.3 64.2 + - - +
286B TRP 3.1 3.9 + - - -
287B HIS* 3.2 25.3 + + - +
288B VAL* 4.0 2.9 + - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLN* 5.7 0.2 - - - -
72B TYR* 3.8 12.9 + - - +
124B TYR* 3.6 23.9 - - - +
154B GLY* 3.6 24.5 - - - -
155B ALA* 4.2 3.0 + - + +
251B LEU* 4.6 6.1 - - - -
281B LEU 3.2 14.5 + - - +
282B VAL* 3.3 15.7 + - - +
283B ASN 3.6 0.2 - - - -
284B HIS* 1.3 76.8 - - - +
286B TRP* 1.3 55.9 + - - +
288B VAL* 3.4 8.8 - - - +
296B ARG* 2.8 33.5 + - - +
298B SER* 2.6 34.7 + - - +
299B PHE* 4.1 21.1 + - + -
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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