Contacts of the helix formed by residues 273 - 283 (chain 3) 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 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1783 LEU* 4.6 1.3 - - - -
2613 LEU 3.8 11.7 - - - -
2623 PHE 4.0 11.9 + - - -
2643 PRO* 4.0 11.3 - - - +
2723 ALA* 1.3 76.4 - - - +
2743 ILE* 1.4 64.8 + - - -
2753 HIS* 3.3 6.8 - - - -
2763 GLU* 2.9 23.9 + - - +
2773 THR* 3.0 12.6 + - - -
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Residues in contact with ILE 274 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1533 LEU* 3.6 26.9 - - + +
1553 SER* 5.7 1.1 - - - +
1603 THR* 3.6 21.3 - - + +
1783 LEU* 3.4 26.4 - - + +
2613 LEU* 3.2 39.2 + - + +
2623 PHE* 3.6 26.0 - - + -
2733 GLY* 1.4 67.1 - - - -
2753 HIS* 1.3 58.9 + - - +
2773 THR* 3.3 7.5 + - + -
2783 THR* 2.9 31.8 + - - -
3093 ILE* 6.2 3.1 - - + -
3133 MET* 3.8 18.6 - - + -
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Residues in contact with HIS 275 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2623 PHE* 3.4 36.3 - + + -
2733 GLY* 2.9 8.0 + - - -
2743 ILE* 1.3 72.5 - - - +
2763 GLU* 1.3 98.1 + - + +
2783 THR* 3.5 3.6 - - - -
2793 TYR* 3.3 20.6 + - - +
3133 MET* 3.4 28.0 - - - -
3163 GLU* 3.2 51.6 + - + -
3173 ILE* 3.8 9.5 - - + +
3203 LEU* 4.9 7.1 - - + +
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Residues in contact with GLU 276 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2723 ALA* 4.1 19.7 - - + +
2733 GLY 2.9 11.9 + - - +
2753 HIS* 1.3 99.4 + - + +
2773 THR* 1.3 54.1 + - - +
2793 TYR* 3.2 7.7 - - - +
2803 ASN* 2.8 52.9 + - - +
3203 LEU* 4.5 13.2 - - + -
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Residues in contact with THR 277 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1603 THR* 6.1 0.4 - - + -
1623 ASN* 2.9 32.3 - - - +
1763 MET* 3.8 20.1 - - + +
1783 LEU* 5.2 15.8 - - + +
2723 ALA* 4.0 18.9 + - - +
2733 GLY 3.0 13.3 + - - -
2743 ILE* 3.5 12.1 - - + +
2763 GLU* 1.3 75.7 - - - +
2783 THR* 1.3 62.6 + - - +
2803 ASN* 3.9 7.9 + - - +
2813 SER* 3.1 23.9 + - - -
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Residues in contact with THR 278 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513 ILE* 3.6 6.6 - - + +
1533 LEU* 3.9 2.6 - - - +
1623 ASN* 3.4 20.2 + - - +
2743 ILE 2.9 14.8 + - - -
2753 HIS 3.5 10.1 - - - -
2773 THR* 1.3 73.9 - - - +
2793 TYR* 1.3 62.3 + - - +
2813 SER* 3.4 3.6 - - - -
2823 ILE* 3.0 35.8 + - + +
2973 ASN* 3.2 34.6 + - - +
3133 MET* 3.0 16.9 - - + +
3173 ILE* 4.1 15.7 - - + -
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Residues in contact with TYR 279 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2753 HIS 3.3 10.0 + - - +
2763 GLU* 3.2 8.7 + - - +
2773 THR 3.1 0.2 - - - -
2783 THR* 1.3 79.1 - - - +
2803 ASN* 1.3 79.9 + - - +
2823 ILE* 2.9 25.7 + - - +
2833 MET* 2.9 56.3 + - + +
2943 TYR* 3.4 20.6 - + - -
3173 ILE* 5.1 5.4 - - + -
3203 LEU* 3.3 62.2 + - + +
3213 ALA 4.3 0.7 - - - -
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Residues in contact with ASN 280 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1763 MET* 4.8 12.6 - - + -
2723 ALA* 4.9 5.2 - - - +
2763 GLU* 2.8 39.9 + - - +
2773 THR* 3.1 9.5 + - - +
2793 TYR* 1.3 91.2 - - - +
2813 SER* 1.3 63.5 + - - +
2833 MET* 3.2 6.1 + - - +
2843 LYS* 3.1 25.5 + - - +
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Residues in contact with SER 281 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513 ILE* 3.6 13.0 - - - -
1623 ASN* 3.6 15.9 - - - +
1643 PRO* 3.4 11.8 - - - +
1743 ALA* 2.4 32.3 + - - +
1763 MET* 3.8 7.8 - - - +
2773 THR 3.1 12.0 + - - -
2783 THR 3.4 11.0 - - - -
2803 ASN* 1.3 73.6 - - - +
2823 ILE* 1.3 59.7 - - - +
2843 LYS* 3.1 24.8 + - - +
2853 CYS* 3.4 14.8 + - - -
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Residues in contact with ILE 282 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513 ILE* 3.7 23.1 - - + -
2783 THR* 3.0 32.5 - - + +
2793 TYR* 2.9 10.2 + - - +
2813 SER* 1.3 80.2 - - - +
2833 MET* 1.3 56.5 + - - +
2843 LYS 3.0 5.1 + - - -
2853 CYS* 3.2 18.7 + - - +
2903 ARG* 3.4 28.9 + - + +
2933 LEU* 4.5 12.8 - - + -
2943 TYR* 3.6 59.5 - - + +
2973 ASN* 4.6 2.0 - - - +
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Residues in contact with MET 283 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2793 TYR* 2.9 57.0 + - + +
2803 ASN* 3.2 7.5 + - - +
2823 ILE* 1.3 70.8 - - - +
2843 LYS* 1.4 56.2 + - - +
2853 CYS 3.5 0.6 - - - +
2903 ARG* 3.9 43.3 + - - +
2943 TYR* 3.4 23.8 - - + +
3223 PRO* 4.0 24.7 - - + -
3253 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