Contacts of the helix formed by residues 273 - 283 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1787 LEU* 4.6 1.3 - - - -
2617 LEU 3.8 11.0 - - - -
2627 PHE 4.0 11.5 + - - -
2647 PRO* 4.0 11.3 - - - +
2727 ALA* 1.3 76.0 - - - +
2747 ILE* 1.3 66.1 + - - -
2757 HIS* 3.3 6.8 - - - -
2767 GLU* 2.9 23.9 + - - +
2777 THR* 3.0 12.2 + - - -
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Residues in contact with ILE 274 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537 LEU* 3.6 26.7 - - + +
1557 SER* 5.5 1.6 - - - +
1607 THR* 3.6 21.1 - - + -
1787 LEU* 3.4 25.8 - - + +
2617 LEU* 3.2 40.3 + - + +
2627 PHE* 3.6 25.8 - - + -
2737 GLY* 1.3 67.2 - - - -
2757 HIS* 1.3 58.5 + - - +
2777 THR* 3.3 7.7 + - + -
2787 THR* 2.9 31.3 + - - -
3097 ILE* 6.2 2.5 - - + -
3137 MET* 3.9 18.2 - - + -
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Residues in contact with HIS 275 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2627 PHE* 3.4 35.9 - + + -
2737 GLY* 2.9 7.8 + - - -
2747 ILE* 1.3 72.7 - - - +
2767 GLU* 1.3 99.0 + - + +
2787 THR* 3.5 3.6 - - - -
2797 TYR* 3.3 20.6 + - - +
3137 MET* 3.4 28.9 - - - -
3167 GLU* 3.2 52.7 + - + -
3177 ILE* 3.8 9.1 - - + +
3207 LEU* 4.9 6.6 - - + +
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Residues in contact with GLU 276 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2727 ALA* 4.1 20.2 - - + +
2737 GLY 2.9 11.3 + - - +
2757 HIS* 1.3 101.5 + - + +
2777 THR* 1.3 53.6 + - - +
2797 TYR* 3.2 8.0 - - - +
2807 ASN* 2.8 52.3 + - - +
3207 LEU* 4.5 13.7 - - + -
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Residues in contact with THR 277 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1607 THR* 6.1 0.7 - - + -
1627 ASN* 2.9 31.4 - - - +
1767 MET* 3.8 20.1 - - + +
1777 ARG 6.0 0.2 - - - -
1787 LEU* 5.2 15.6 - - + +
2727 ALA* 4.0 18.7 + - - +
2737 GLY 3.0 14.1 + - - -
2747 ILE* 3.5 11.9 - - + +
2767 GLU* 1.3 75.0 - - - +
2787 THR* 1.3 64.0 + - - +
2807 ASN* 3.8 7.7 + - - +
2817 SER* 3.1 24.4 + - - -
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Residues in contact with THR 278 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517 ILE* 3.6 6.9 - - + +
1537 LEU* 3.9 2.8 - - - +
1627 ASN* 3.4 19.6 + - - +
2747 ILE 2.9 15.0 + - - -
2757 HIS 3.5 9.9 - - - -
2777 THR* 1.3 74.1 - - - +
2797 TYR* 1.3 62.6 + - - +
2817 SER* 3.4 3.8 - - - -
2827 ILE* 3.0 35.7 + - + +
2977 ASN* 3.2 34.6 + - - +
3137 MET* 3.0 17.6 - - + +
3177 ILE* 4.1 15.7 - - + -
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Residues in contact with TYR 279 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2757 HIS 3.3 9.4 + - - +
2767 GLU* 3.2 8.3 - - - +
2787 THR* 1.3 79.5 - - - +
2807 ASN* 1.3 79.1 + - - +
2827 ILE* 2.9 26.0 + - - +
2837 MET* 2.9 55.5 + - + +
2947 TYR* 3.4 20.9 - + - -
3177 ILE* 5.1 6.1 - - + -
3207 LEU* 3.3 63.3 + - + +
3217 ALA 4.5 0.7 - - - -
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Residues in contact with ASN 280 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1767 MET* 4.8 12.6 - - + -
2727 ALA* 4.9 5.0 - - - +
2767 GLU* 2.8 41.2 + - - +
2777 THR* 3.1 9.9 + - - +
2797 TYR* 1.3 90.9 - - - +
2817 SER* 1.3 63.9 + - - +
2837 MET* 3.2 6.0 + - - +
2847 LYS* 3.1 26.0 + - - +
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Residues in contact with SER 281 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517 ILE* 3.6 12.8 - - - -
1627 ASN* 3.6 16.7 - - - +
1647 PRO* 3.4 12.1 - - - +
1747 ALA* 2.4 32.2 + - - +
1767 MET* 3.8 7.7 - - - +
2777 THR 3.1 11.1 + - - -
2787 THR 3.4 10.5 - - - -
2807 ASN* 1.3 73.9 - - - +
2827 ILE* 1.3 58.6 + - - +
2847 LYS* 3.1 24.5 + - - +
2857 CYS* 3.4 15.3 + - - -
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Residues in contact with ILE 282 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517 ILE* 3.7 22.2 - - + -
2787 THR* 3.0 32.5 - - + +
2797 TYR* 2.9 10.5 + - - +
2817 SER* 1.3 80.5 - - - +
2837 MET* 1.3 55.6 + - - +
2847 LYS 3.0 5.4 + - - -
2857 CYS* 3.2 18.5 + - - +
2907 ARG* 3.4 28.8 + - + +
2937 LEU* 4.5 12.8 - - + -
2947 TYR* 3.6 58.1 - - + +
2977 ASN* 4.6 2.0 - - - +
3177 ILE* 5.3 0.2 - - + -
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Residues in contact with MET 283 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2797 TYR* 2.9 56.2 + - + +
2807 ASN* 3.2 6.8 + - - +
2827 ILE* 1.3 70.5 - - - +
2847 LYS* 1.4 56.3 + - - +
2857 CYS 3.5 0.6 - - - +
2907 ARG* 3.9 42.4 + - - +
2947 TYR* 3.4 25.1 - - + +
3227 PRO* 4.0 24.5 - - + -
3257 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