Contacts of the helix formed by residues 289 - 295 (chain 2) 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 ILE 289 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1662 TYR* 3.7 39.5 - - + -
1712 LEU* 3.6 33.4 - - + -
2852 CYS* 4.0 7.4 - - + -
2862 ASP* 3.1 43.3 + - + +
2872 ILE 3.2 0.4 - - - -
2882 ASP* 1.4 77.1 - - + +
2902 ARG* 1.3 65.2 + - - +
2912 LYS* 3.3 6.5 - - - +
2922 ASP* 3.0 17.8 + - - +
2932 LEU* 3.3 30.1 + - + +
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Residues in contact with ARG 290 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2822 ILE* 3.4 36.1 + - + +
2832 MET* 3.9 47.2 + - - +
2852 CYS* 2.4 32.8 + - + -
2862 ASP 3.3 9.8 + - - +
2872 ILE* 3.5 11.1 + - + +
2882 ASP 3.4 1.6 - - - -
2892 ILE* 1.3 77.7 - - - +
2912 LYS* 1.4 62.2 + - - +
2922 ASP 3.3 0.3 + - - -
2932 LEU* 4.1 7.3 - - - +
2942 TYR* 3.1 33.0 + - + -
3252 MET* 4.7 5.8 - - + -
2014 VAL* 5.5 1.8 - - - +
2024 THR* 1.5 48.2 + - - +
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Residues in contact with LYS 291 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2872 ILE 4.7 2.5 + - - +
2882 ASP* 3.0 30.1 + - - +
2892 ILE* 3.2 1.2 + - - +
2902 ARG* 1.4 75.8 - - - +
2922 ASP* 1.4 97.6 + - - +
2942 TYR* 3.4 2.4 + - - +
2952 ALA* 3.2 23.6 + - - +
3252 MET* 3.7 24.4 - - + +
3262 LYS* 4.5 2.1 - - - +
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Residues in contact with ASP 292 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492 THR* 3.9 22.6 - - + +
1662 TYR* 4.0 20.4 + - - -
2892 ILE* 3.0 9.8 + - - +
2912 LYS* 1.4 104.5 + - - +
2932 LEU* 1.3 67.9 + - - +
2952 ALA* 3.1 5.2 + - - -
2962 ASN* 2.9 32.5 + - - +
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Residues in contact with LEU 293 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492 THR* 3.8 23.1 - - + -
1502 GLY* 3.8 19.7 - - - +
1512 ILE* 3.4 30.6 - - + +
1642 PRO* 4.4 7.0 - - + -
1652 ILE 4.3 4.7 - - - +
2822 ILE* 4.5 18.6 - - + -
2852 CYS* 4.0 21.5 - - + -
2892 ILE* 3.3 42.1 + - + +
2902 ARG* 4.1 6.5 - - - +
2922 ASP* 1.3 76.8 - - - +
2942 TYR* 1.3 62.3 + - - +
2962 ASN 3.0 21.3 + - - -
2972 ASN* 3.7 1.2 + - - +
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Residues in contact with TYR 294 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2792 TYR* 3.4 19.3 - + - -
2822 ILE* 3.6 36.3 - - + +
2832 MET* 3.4 31.9 - - + +
2902 ARG* 3.1 29.3 + - + +
2912 LYS 3.7 3.6 - - - +
2922 ASP 3.2 1.0 - - - -
2932 LEU* 1.3 79.4 - - - +
2952 ALA* 1.3 59.0 + - - +
2962 ASN 3.1 1.1 + - - -
2972 ASN* 4.6 2.4 + - - +
3172 ILE* 4.0 19.1 - - + +
3212 ALA* 3.6 20.9 - - + +
3222 PRO* 4.7 0.2 - - + -
3252 MET* 3.4 31.4 - - + -
3262 LYS 3.2 15.0 - - - +
3272 ILE* 3.4 17.4 - - + -
3282 LYS 2.8 22.2 + - - +
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Residues in contact with ALA 295 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1472 ARG* 4.6 0.2 + - - -
2912 LYS 3.2 11.5 + - - +
2922 ASP* 3.1 3.2 + - - -
2942 TYR* 1.3 77.4 - - - +
2962 ASN* 1.3 75.4 + - - +
3262 LYS* 3.8 33.0 - - + +
3282 LYS* 3.2 35.5 - - + +
3302 ILE* 3.8 0.9 - - - +
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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