Contacts of the helix formed by residues 26 - 39 (chain 2) in PDB entry 6Q8O
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 ALA 26 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142 THR* 5.5 6.7 - - - +
152 PHE* 3.7 31.2 - - + -
182 TYR* 4.4 9.2 - - + -
232 ARG 2.9 15.3 + - - +
252 ALA* 1.3 76.5 - - - +
272 ILE* 1.3 61.6 + - - +
282 MET 3.2 0.4 - - - -
292 PRO* 3.1 12.6 - - + +
302 LEU* 3.1 39.3 + - + +
532 VAL* 4.3 2.9 - - + -
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Residues in contact with ILE 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1941 GLY* 4.9 3.4 - - - +
242 ARG* 3.1 34.5 - - + +
252 ALA 2.8 2.4 + - - -
262 ALA* 1.3 78.1 - - - +
282 MET* 1.3 62.2 + - + +
312 LEU* 3.2 50.1 + - + +
492 ILE* 3.8 17.0 - - + -
532 VAL* 3.7 27.6 - - + -
552 THR* 4.2 4.0 - - + -
602 VAL* 3.7 40.4 - - + -
632 VAL* 4.2 15.7 - - + -
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Residues in contact with MET 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331 TYR* 4.9 1.6 - - - +
1741 HIS* 3.8 23.3 - - + +
1751 ARG 4.8 6.4 - - - +
1761 GLY* 4.6 7.0 - - - -
1771 ALA* 4.2 22.2 - - + +
1911 SER* 3.5 39.3 - - - +
1941 GLY* 5.2 3.8 - - - -
1951 LEU 5.6 0.4 - - - +
252 ALA 2.9 11.6 + - - +
272 ILE* 1.3 78.5 - - + +
292 PRO* 1.3 66.7 - - + +
312 LEU* 4.7 2.5 - - - -
322 ARG* 3.6 3.1 + - - +
632 VAL* 5.0 12.3 - - + -
672 TYR* 3.6 35.0 - - + -
702 TYR* 2.3 36.2 + - + +
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Residues in contact with PRO 29 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1741 HIS* 4.5 8.5 - - + -
1751 ARG* 5.3 10.5 - - + +
102 PHE* 5.8 3.4 - - + -
142 THR* 5.4 14.6 - - + -
172 LYS* 5.4 7.4 - - + +
182 TYR* 4.7 13.2 - - + +
252 ALA 3.3 10.1 - - - +
262 ALA* 3.1 22.2 - - + +
282 MET* 1.3 92.0 - - + +
302 LEU* 1.3 67.0 + - + +
322 ARG* 2.9 20.0 + - + +
332 ARG* 3.1 14.5 + - - +
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Residues in contact with LEU 30 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 PHE* 3.5 39.6 - - + -
102 PHE* 3.8 18.6 - - + -
112 LEU* 4.8 9.9 - - + -
142 THR* 4.5 16.6 - - + +
152 PHE* 5.1 9.6 - - + -
262 ALA* 3.1 38.9 + - + +
272 ILE 4.2 0.4 - - - +
292 PRO* 1.3 75.9 - - + +
312 LEU* 1.3 66.0 + - - +
332 ARG* 2.9 21.3 + - - +
342 VAL* 3.4 8.0 + - - +
492 ILE* 3.9 29.4 - - + +
522 LEU* 5.3 5.4 - - + -
532 VAL* 5.8 1.8 - - + -
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Residues in contact with LEU 31 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272 ILE* 3.2 40.0 + - + +
282 MET* 4.7 0.9 - - - -
302 LEU* 1.3 76.1 - - - +
322 ARG* 1.3 63.4 + - - +
342 VAL* 2.9 18.9 + - - +
352 GLN 3.0 8.8 + - - -
412 ILE* 3.7 33.2 - - + +
462 ILE* 4.2 9.0 - - + -
492 ILE* 3.5 22.5 - - + +
602 VAL* 4.9 2.0 - - + -
632 VAL* 4.9 2.7 - - + -
642 ALA* 3.6 28.3 - - + +
702 TYR* 3.4 35.4 - - + -
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Residues in contact with ARG 32 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361 GLY* 3.3 16.3 + - - -
1751 ARG* 2.9 66.6 + - - +
1761 GLY 2.4 32.3 + - - -
1771 ALA* 3.9 1.2 - - - +
282 MET 3.8 8.7 + - - +
292 PRO* 2.9 15.7 + - + +
312 LEU* 1.3 78.5 - - - +
332 ARG* 1.3 62.6 + - + +
352 GLN* 2.9 21.3 + - + +
362 GLN* 3.3 12.7 + - + +
692 TYR* 3.1 47.8 + - - -
702 TYR* 3.5 16.8 + - + +
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Residues in contact with ARG 33 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 PHE* 5.2 3.9 - - + -
42 PHE* 5.3 4.7 - - + -
72 LYS* 3.1 40.8 - - - +
102 PHE* 3.4 45.6 - - + +
292 PRO 3.1 7.8 + - - +
302 LEU* 2.9 12.1 + - - +
322 ARG* 1.3 78.9 - - + +
342 VAL* 1.3 62.9 + - + +
362 GLN* 3.7 19.3 + - - +
372 GLU* 2.8 68.0 + - - +
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Residues in contact with VAL 34 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 PHE* 3.6 30.7 - - + -
42 PHE* 5.0 0.4 - - + -
302 LEU 3.8 9.6 - - - +
312 LEU* 2.9 14.8 + - - +
332 ARG* 1.3 75.8 - - - +
352 GLN* 1.3 63.6 + - - +
372 GLU* 2.9 5.6 + - - -
382 GLU* 2.9 34.8 + - + +
392 GLY 3.9 0.7 + - - -
402 TRP 3.9 18.1 - - - +
412 ILE* 4.0 11.4 - - + -
452 ARG* 4.0 34.3 - - + -
492 ILE* 5.0 4.0 - - + -
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Residues in contact with GLN 35 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 LEU 3.0 6.3 + - - +
322 ARG* 2.9 22.9 + - + +
342 VAL* 1.3 75.3 - - - +
362 GLN* 1.3 62.9 + - + +
392 GLY* 2.8 60.0 + - - +
402 TRP* 4.9 0.4 - - - +
412 ILE* 4.4 6.7 - - + +
692 TYR* 3.5 46.3 + - + +
702 TYR* 4.2 13.5 - - + -
712 GLN* 4.7 5.9 + - - +
792 HIS* 5.7 1.7 - - - -
1372 ASN* 3.4 35.1 + - - +
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Residues in contact with GLN 36 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 ARG* 4.3 24.0 + - - +
1751 ARG* 4.3 11.4 + - - -
322 ARG* 3.3 11.4 + - + +
332 ARG* 4.0 26.4 - - - +
352 GLN* 1.3 87.4 - - - +
372 GLU* 1.3 68.8 + - + +
392 GLY 4.4 1.5 + - - -
692 TYR* 5.8 0.4 - - - +
1372 ASN* 4.8 3.6 - - - +
1382 ASP* 4.7 19.7 - - + +
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Residues in contact with GLU 37 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 PHE* 5.4 11.4 - - + -
72 LYS* 4.7 5.5 + - - +
332 ARG* 2.8 54.7 + - - +
342 VAL* 2.9 8.3 + - - +
362 GLN* 1.3 87.4 + - + +
382 GLU* 1.3 68.5 + - + +
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Residues in contact with GLU 38 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 PHE* 5.5 6.2 - - + -
342 VAL* 2.9 18.8 + - + +
372 GLU* 1.3 84.2 - - + +
392 GLY* 1.3 56.6 + - - +
402 TRP* 3.1 35.0 + - + +
422 ARG* 2.6 47.7 + - - +
452 ARG* 4.6 14.0 + - - -
752 THR* 5.0 2.6 - - - +
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Residues in contact with GLY 39 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 GLN* 2.8 35.4 + - - +
362 GLN 4.4 1.2 - - - -
372 GLU 3.7 0.4 - - - -
382 GLU* 1.3 76.8 - - - +
402 TRP* 1.3 60.2 + - - +
712 GLN* 3.6 8.0 - - - +
752 THR* 3.3 27.3 - - - +
792 HIS* 5.5 0.3 - - - -
1372 ASN* 5.2 8.1 + - - -
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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
------------------------------------------------------------
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