Contacts of the helix formed by residues 289 - 295 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664 TYR* 3.7 39.0 - - + -
1714 LEU* 3.6 33.2 - - + -
2854 CYS* 4.0 7.6 - - + -
2864 ASP* 3.1 42.4 + - + +
2874 ILE 3.2 0.6 - - - -
2884 ASP* 1.4 77.1 - - + +
2904 ARG* 1.3 65.8 + - - +
2914 LYS* 3.3 6.5 - - - +
2924 ASP* 3.0 17.7 + - - +
2934 LEU* 3.3 31.0 + - + +
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Residues in contact with ARG 290 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2824 ILE* 3.4 36.9 + - + +
2834 MET* 3.9 46.0 + - - +
2854 CYS* 2.4 32.6 + - + -
2864 ASP 3.3 9.4 + - - +
2874 ILE* 3.8 11.8 - - + +
2884 ASP 3.4 1.6 - - - -
2894 ILE* 1.3 78.3 - - - +
2914 LYS* 1.4 61.7 + - - +
2924 ASP 3.3 0.2 + - - -
2934 LEU* 4.1 8.1 - - - +
2944 TYR* 3.1 32.6 + - + -
3254 MET* 4.7 5.2 - - + -
2016 VAL* 5.3 4.6 - - - +
2026 THR* 1.6 46.1 + - - +
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Residues in contact with LYS 291 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2874 ILE 4.7 2.1 + - - +
2884 ASP* 3.0 29.9 + - - +
2894 ILE* 3.2 0.8 + - - +
2904 ARG* 1.4 75.0 - - - +
2924 ASP* 1.4 97.0 + - - +
2944 TYR* 3.4 3.3 + - - +
2954 ALA* 3.2 23.0 + - - +
3254 MET* 3.7 24.0 - - + +
3264 LYS* 4.5 2.3 - - - +
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Residues in contact with ASP 292 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494 THR* 3.9 22.4 - - + +
1664 TYR* 4.0 20.6 + - - -
2894 ILE* 3.0 9.6 + - - +
2914 LYS* 1.4 103.5 + - - +
2934 LEU* 1.3 67.6 + - - +
2954 ALA* 3.1 5.0 + - - -
2964 ASN* 2.9 31.9 + - - +
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Residues in contact with LEU 293 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494 THR* 3.8 22.9 - - + -
1504 GLY* 3.8 20.6 - - - +
1514 ILE* 3.4 30.6 - - + +
1644 PRO* 4.4 6.1 - - + -
1654 ILE 4.3 4.9 - - - +
2824 ILE* 4.5 17.7 - - + -
2854 CYS* 4.0 22.0 - - + -
2894 ILE* 3.3 42.5 + - + +
2904 ARG* 4.1 6.7 - - - +
2924 ASP* 1.3 77.3 - - - +
2944 TYR* 1.3 63.6 + - - +
2964 ASN 3.0 21.3 + - - -
2974 ASN* 3.7 1.2 + - - +
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Residues in contact with TYR 294 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2794 TYR* 3.4 18.9 - + - -
2824 ILE* 3.6 36.7 - - + +
2834 MET* 3.4 32.9 - - + +
2904 ARG* 3.1 28.2 + - + +
2914 LYS 3.7 4.0 - - - +
2924 ASP 3.2 1.2 - - - -
2934 LEU* 1.3 78.8 - - - +
2954 ALA* 1.3 59.7 + - - +
2964 ASN 3.4 0.7 + - - -
2974 ASN* 4.6 1.8 + - - +
3174 ILE* 4.0 20.3 - - + +
3214 ALA* 3.6 21.2 - - + +
3224 PRO* 4.7 0.2 - - + -
3254 MET* 3.4 32.3 - - + -
3264 LYS 3.2 15.3 - - - +
3274 ILE* 3.4 17.9 - - + -
3284 LYS 2.8 21.7 + - - +
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Residues in contact with ALA 295 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2914 LYS 3.2 11.5 + - - +
2924 ASP* 3.1 3.5 + - - +
2944 TYR* 1.3 78.5 - - - +
2964 ASN* 1.4 74.8 + - - +
3264 LYS* 3.8 32.3 - - + +
3284 LYS* 3.2 34.3 - - + +
3304 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