Contacts of the helix formed by residues 273 - 283 (chain 6) in PDB entry 1MVW
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 GLY 273 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1786 LEU* 4.6 1.6 - - - -
2616 LEU 3.8 10.5 - - - -
2626 PHE 4.0 12.1 + - - -
2646 PRO* 4.0 11.8 - - - +
2726 ALA* 1.3 76.9 - - - +
2746 ILE* 1.4 64.9 + - - -
2756 HIS* 3.3 6.4 - - - -
2766 GLU* 2.9 23.8 + - - +
2776 THR* 3.0 12.4 + - - -
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Residues in contact with ILE 274 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1536 LEU* 3.6 27.6 - - + +
1556 SER* 5.5 1.3 - - - +
1606 THR* 3.6 21.3 - - + -
1786 LEU* 3.4 25.6 - - + -
2616 LEU* 3.2 40.1 + - + +
2626 PHE* 3.6 25.8 - - + -
2736 GLY* 1.4 66.8 - - - -
2756 HIS* 1.3 57.9 + - - +
2776 THR* 3.3 7.0 + - + -
2786 THR* 2.9 31.4 + - - -
3096 ILE* 6.2 2.9 - - + -
3136 MET* 3.9 19.1 - - + -
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Residues in contact with HIS 275 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2626 PHE* 3.4 34.7 - + + -
2736 GLY* 2.9 8.0 + - - -
2746 ILE* 1.3 71.4 - - - +
2766 GLU* 1.3 98.0 + - + +
2786 THR* 3.5 3.3 - - - -
2796 TYR* 3.3 21.3 + - - +
3136 MET* 3.4 30.3 - - - -
3166 GLU* 3.2 54.4 + - + -
3176 ILE* 3.8 8.4 - - + +
3206 LEU* 4.9 7.5 - - + +
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Residues in contact with GLU 276 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2726 ALA* 4.1 20.5 - - + +
2736 GLY 2.9 12.6 + - - +
2756 HIS* 1.3 100.7 + - + +
2776 THR* 1.3 53.0 + - - +
2796 TYR* 3.2 7.9 - - - +
2806 ASN* 2.8 51.7 + - - +
3206 LEU* 4.5 14.4 - - + -
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Residues in contact with THR 277 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1606 THR* 6.1 0.4 - - + -
1626 ASN* 2.9 31.4 + - - +
1766 MET* 3.8 19.8 - - + +
1786 LEU* 5.2 16.2 - - + +
2726 ALA* 4.0 18.9 + - - +
2736 GLY 3.0 13.6 + - - -
2746 ILE* 3.5 12.6 - - + +
2766 GLU* 1.3 74.0 - - - +
2786 THR* 1.3 65.2 + - - +
2806 ASN* 3.1 8.6 + - - +
2816 SER* 3.1 23.7 + - - -
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Residues in contact with THR 278 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516 ILE* 3.6 6.5 - - + +
1536 LEU* 3.9 2.8 - - - +
1626 ASN* 3.4 19.8 + - - +
2746 ILE 2.9 15.1 + - - -
2756 HIS 3.5 9.9 - - - -
2776 THR* 1.3 72.7 - - - +
2796 TYR* 1.3 63.4 + - - +
2816 SER* 3.4 4.3 - - - -
2826 ILE* 3.0 35.8 + - + +
2976 ASN* 3.2 33.9 + - - +
3136 MET* 3.0 17.5 - - + +
3176 ILE* 4.1 15.9 - - + -
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Residues in contact with TYR 279 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2756 HIS 3.3 10.3 + - - +
2766 GLU 3.2 8.0 + - - +
2786 THR* 1.3 79.7 - - - +
2806 ASN* 1.3 79.4 + - - +
2826 ILE* 2.9 25.6 + - - +
2836 MET* 2.9 55.4 + - + +
2946 TYR* 3.4 20.9 - + - -
3176 ILE* 5.1 6.3 - - + -
3206 LEU* 3.3 62.6 + - + +
3216 ALA 4.5 0.4 - - - -
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Residues in contact with ASN 280 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1766 MET* 4.8 13.2 - - - -
2726 ALA* 4.9 5.2 - - - +
2766 GLU* 2.8 40.0 + - - +
2776 THR* 3.1 9.6 + - - +
2796 TYR* 1.3 94.2 - - - +
2816 SER* 1.3 61.4 + - - +
2836 MET* 3.2 6.1 + - - +
2846 LYS* 3.1 26.0 + - - +
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Residues in contact with SER 281 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516 ILE* 3.6 13.2 - - - -
1626 ASN* 3.6 17.7 - - - +
1646 PRO* 3.4 12.2 - - - +
1746 ALA* 2.4 31.5 + - - +
1766 MET* 3.8 7.7 - - - +
2776 THR 3.1 11.1 + - - -
2786 THR 3.4 11.4 - - - -
2806 ASN* 1.3 75.5 - - - +
2826 ILE* 1.3 58.3 + - - +
2846 LYS* 3.1 24.5 + - - +
2856 CYS* 3.4 14.8 + - - -
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Residues in contact with ILE 282 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516 ILE* 3.7 22.9 - - + -
2786 THR* 3.0 32.5 - - + +
2796 TYR* 2.9 11.6 + - - +
2816 SER* 1.3 80.8 - - - +
2836 MET* 1.3 56.1 + - - +
2846 LYS 3.0 5.1 + - - -
2856 CYS* 3.2 19.4 + - - +
2906 ARG* 3.4 27.8 + - + +
2936 LEU* 4.5 13.7 - - + -
2946 TYR* 3.6 58.3 - - + +
2976 ASN* 4.6 1.8 - - - +
3176 ILE* 5.3 0.2 - - + -
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Residues in contact with MET 283 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2796 TYR* 2.9 58.4 + - + +
2806 ASN* 3.2 7.0 + - - +
2826 ILE* 1.3 68.5 - - - +
2846 LYS* 1.4 55.0 + - - +
2856 CYS 3.5 1.1 - - - +
2906 ARG* 3.9 42.6 + - - +
2946 TYR* 3.4 24.2 - - + +
3226 PRO* 4.0 25.1 - - + -
3256 MET* 6.0 0.7 - - + -
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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