Contacts of the helix formed by residues 271 - 278 (chain 1) 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 THR 271 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2691 GLY 4.7 1.8 - - - +
2701 THR* 1.3 77.7 + - - +
2721 PHE* 1.3 65.0 + - - +
2731 ARG* 4.0 4.0 + - - +
2741 GLU* 3.3 23.0 + - - +
2751 LEU* 3.1 19.9 + - - +
3071 LEU 3.5 11.9 - - - -
3081 ASP* 3.6 29.4 + - + +
3091 THR 3.2 12.3 - - - +
3101 PRO* 4.2 7.9 - - + -
3111 MET* 4.6 0.2 - - - -
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Residues in contact with PHE 272 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2711 THR* 1.3 73.0 - - - +
2731 ARG* 1.3 62.8 + - - +
2751 LEU* 3.2 6.9 + - + +
2761 ILE* 2.9 39.4 + - + +
2901 ILE* 4.3 18.8 - - + -
2921 PRO* 4.0 17.9 - - + -
3001 LEU* 5.4 3.4 - - + -
3061 VAL* 3.3 18.6 - - + -
3071 LEU* 2.9 23.6 + - + +
3091 THR* 3.0 47.1 - - + -
3111 MET* 3.6 43.5 - - + -
3161 LEU* 4.1 22.2 - - + -
3281 VAL* 5.7 4.7 - - + -
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Residues in contact with ARG 273 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2711 THR* 3.2 5.6 - - - +
2721 PHE* 1.3 78.0 - - - +
2741 GLU* 1.3 56.6 + - - +
2771 TYR* 2.9 61.1 + - + +
3041 GLU* 2.4 58.1 + - - +
3071 LEU* 3.0 27.4 + - + +
3081 ASP* 2.3 40.9 + - - +
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Residues in contact with GLU 274 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 SER 4.2 8.5 - - - +
81 GLY* 3.5 23.4 - - - -
91 LEU* 4.1 4.3 + - - +
2701 THR* 3.8 16.5 - - - +
2711 THR* 3.3 22.1 + - - +
2731 ARG* 1.3 80.2 - - - +
2751 LEU* 1.3 62.4 + - - +
2771 TYR* 5.2 0.2 - - - -
2781 GLU* 2.9 39.9 + - + +
2791 TRP* 3.0 34.8 + - - +
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Residues in contact with LEU 275 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2521 TYR* 3.7 28.5 - - + -
2531 GLN 5.9 1.3 - - - +
2541 ILE* 4.6 29.8 - - + -
2641 TYR* 5.4 7.0 - - + -
2661 LEU* 5.0 7.0 - - + -
2701 THR* 4.3 8.5 - - - +
2711 THR 3.1 10.8 + - - +
2721 PHE* 3.2 9.2 + - + +
2741 GLU* 1.3 80.5 - - - +
2761 ILE* 1.3 60.4 + - + +
2791 TRP* 3.1 27.0 - - + +
2801 ALA* 2.9 23.8 + - + -
3111 MET* 3.5 33.2 - - + -
3281 VAL* 4.9 7.2 - - + -
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Residues in contact with ILE 276 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2541 ILE* 4.3 13.9 - - + -
2581 VAL* 4.8 0.9 - - + -
2721 PHE* 2.9 26.4 + - + +
2731 ARG 4.2 0.9 - - - +
2751 LEU* 1.3 80.1 - - + +
2771 TYR* 1.3 65.2 + - + +
2801 ALA* 3.1 15.3 - - + +
2811 GLY 3.1 9.7 + - - -
2821 GLY* 2.8 20.6 + - - -
2831 PRO* 4.1 29.6 - - + -
2901 ILE* 4.9 12.1 - - + -
3021 PHE* 4.6 10.1 - - + -
3071 LEU* 3.7 26.2 - - + -
3281 VAL* 6.0 2.2 - - + -
3301 LEU* 4.5 17.5 - - + -
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Residues in contact with TYR 277 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2601 ARG* 4.9 0.2 + - - -
2731 ARG* 2.9 54.5 + - + +
2741 GLU* 5.2 0.2 - - - -
2761 ILE* 1.3 81.1 - - + +
2781 GLU* 1.3 67.3 + - + +
2811 GLY* 3.2 22.3 + - - -
2821 GLY* 3.6 13.7 - - - +
2831 PRO* 3.5 28.1 - - + +
3021 PHE* 4.8 12.2 - + - -
3041 GLU* 5.3 2.5 + - - -
3071 LEU* 4.9 11.5 - - + +
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Residues in contact with GLU 278 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91 LEU* 5.4 12.9 - - + +
2601 ARG* 4.2 8.8 + - - -
2741 GLU* 2.9 32.9 + - + +
2771 TYR* 1.3 80.6 - - + +
2791 TRP* 1.3 75.0 + - + +
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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