Contacts of the helix formed by residues 273 - 283 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1789 LEU* 4.6 1.1 - - - -
2619 LEU 3.8 11.0 - - - -
2629 PHE 4.0 10.4 + - - -
2649 PRO* 4.0 12.2 - - - +
2729 ALA* 1.3 76.7 - - - +
2749 ILE* 1.3 66.7 + - - -
2759 HIS* 3.3 6.9 - - - -
2769 GLU* 2.9 23.7 + - - +
2779 THR* 3.0 12.5 + - - -
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Residues in contact with ILE 274 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539 LEU* 3.6 27.7 - - + +
1559 SER* 5.7 0.9 - - - +
1609 THR* 3.6 21.1 - - + -
1789 LEU* 3.4 26.2 - - + +
2619 LEU* 3.2 39.8 + - + +
2629 PHE* 3.6 25.4 - - + -
2739 GLY* 1.3 66.8 - - - -
2759 HIS* 1.3 58.3 + - - +
2779 THR* 3.3 7.1 + - + -
2789 THR* 2.9 31.5 + - - -
3099 ILE* 6.2 2.7 - - + -
3139 MET* 3.9 18.2 - - + -
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Residues in contact with HIS 275 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2629 PHE* 3.4 35.3 - + + -
2739 GLY* 2.9 8.6 + - - -
2749 ILE* 1.3 71.6 - - - +
2769 GLU* 1.3 97.6 + - + +
2789 THR* 3.5 3.8 - - - -
2799 TYR* 3.3 20.6 + - - +
3139 MET* 3.4 29.2 - - - -
3169 GLU* 3.2 53.3 + - + -
3179 ILE* 3.8 9.1 - - + +
3209 LEU* 4.9 7.0 - - + +
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Residues in contact with GLU 276 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2729 ALA* 4.1 21.1 - - + +
2739 GLY 2.9 12.1 + - - +
2759 HIS* 1.3 101.2 + - + +
2779 THR* 1.3 53.8 + - - +
2799 TYR* 3.2 8.0 - - - +
2809 ASN* 2.8 51.4 + - - +
3209 LEU* 4.5 13.9 - - + -
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Residues in contact with THR 277 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539 LEU* 5.9 0.2 - - + -
1609 THR* 6.1 0.2 - - + -
1629 ASN* 2.9 31.4 - - - +
1769 MET* 3.8 18.8 - - + +
1789 LEU* 5.2 16.1 - - + +
2729 ALA* 4.0 18.9 + - - +
2739 GLY 3.0 14.0 + - - -
2749 ILE* 3.5 11.4 - - + +
2769 GLU* 1.3 75.5 - - - +
2789 THR* 1.3 63.9 + - - +
2809 ASN* 3.8 7.8 + - - +
2819 SER* 3.1 24.3 + - - -
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Residues in contact with THR 278 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1519 ILE* 3.6 6.4 - - + +
1539 LEU* 3.9 3.3 - - - +
1629 ASN* 3.4 19.6 + - - +
2749 ILE 2.9 15.2 + - - -
2759 HIS 3.5 9.9 - - - -
2779 THR* 1.3 73.7 - - - +
2799 TYR* 1.3 61.7 + - - +
2819 SER* 3.4 4.2 - - - -
2829 ILE* 3.0 35.9 + - + +
2979 ASN* 3.2 34.9 + - - +
3139 MET* 3.0 17.2 - - + +
3179 ILE* 4.1 15.7 - - + -
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Residues in contact with TYR 279 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2759 HIS 3.3 9.4 + - - +
2769 GLU 3.2 8.0 + - - +
2789 THR* 1.3 79.7 - - - +
2809 ASN* 1.3 79.1 + - - +
2829 ILE* 2.9 24.9 + - - +
2839 MET* 2.9 55.9 + - + +
2949 TYR* 3.4 20.6 - + - -
3179 ILE* 5.1 5.4 - - + -
3209 LEU* 3.3 62.4 + - + +
3219 ALA* 4.5 0.7 - - + -
3229 PRO* 5.7 0.2 - - - +
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Residues in contact with ASN 280 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1769 MET* 4.8 12.8 - - - -
2729 ALA* 4.9 5.4 - - - +
2769 GLU* 2.8 40.2 + - - +
2779 THR* 3.1 8.8 + - - +
2799 TYR* 1.3 92.2 - - - +
2819 SER* 1.3 61.7 - - - +
2839 MET* 3.2 6.6 + - - +
2849 LYS* 3.1 26.0 + - - +
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Residues in contact with SER 281 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519 ILE* 3.6 13.5 - - - -
1629 ASN* 3.6 16.1 + - - +
1649 PRO* 3.4 11.7 - - - +
1749 ALA* 2.4 31.7 + - - +
1769 MET* 3.8 7.4 - - - +
2779 THR 3.1 11.6 + - - -
2789 THR 3.4 11.7 - - - -
2809 ASN* 1.3 74.0 - - - +
2829 ILE* 1.3 59.4 - - - +
2849 LYS* 3.1 25.1 + - - +
2859 CYS* 3.4 14.8 + - - -
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Residues in contact with ILE 282 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519 ILE* 3.7 23.3 - - + -
2789 THR* 3.0 32.3 - - + +
2799 TYR* 2.9 11.7 + - - +
2819 SER* 1.3 79.9 - - - +
2839 MET* 1.3 56.0 + - - +
2849 LYS 3.0 5.7 + - - -
2859 CYS* 3.2 18.6 + - - +
2909 ARG* 3.4 28.0 + - + +
2939 LEU* 4.5 13.5 - - + -
2949 TYR* 3.6 59.2 - - + +
2979 ASN* 4.6 2.0 - - - +
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Residues in contact with MET 283 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2799 TYR* 2.9 58.5 + - + +
2809 ASN* 3.2 7.0 + - - +
2829 ILE* 1.3 69.6 - - - +
2849 LYS* 1.4 57.0 + - - +
2859 CYS 3.5 0.6 - - - +
2909 ARG* 3.9 42.9 + - - +
2949 TYR* 3.4 25.1 - - + +
3229 PRO* 4.0 24.2 - - + -
3259 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