Contacts of the helix formed by residues 252 - 257 (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 ASN 252 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1967 ARG* 3.5 19.2 + - - -
2277 MET* 5.7 1.3 - - - -
2307 ALA* 3.3 43.4 + - + +
2337 SER* 5.0 1.6 + - - -
2367 LEU* 3.9 11.5 - - - +
2377 GLU* 4.0 10.4 + - - +
2517 GLY* 1.3 76.3 - - - +
2537 GLU* 1.4 58.6 + - - +
2547 ARG* 2.8 15.9 + - - +
2557 PHE* 3.1 36.9 + - + -
2567 ARG* 3.8 13.8 - - - +
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Residues in contact with GLU 253 (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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1897 LEU* 4.6 5.9 - - + +
1927 ILE* 3.6 28.0 - - + +
1937 LEU* 4.1 16.8 - - + -
1967 ARG* 3.3 40.0 + - - +
2507 ILE* 3.5 11.8 - - + -
2517 GLY 3.0 28.8 + - - -
2527 ASN* 1.4 70.3 + - - +
2547 ARG* 1.3 66.2 + - - +
2557 PHE 3.1 0.7 - - - -
2567 ARG* 3.0 43.9 + - - +
2577 CYS* 3.1 17.7 + - - +
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Residues in contact with ARG 254 (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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1897 LEU* 5.7 0.4 - - - -
2157 LYS 5.4 0.2 + - - -
2167 LEU* 2.9 33.4 + - + +
2177 CYS* 2.9 30.0 - - - +
2187 TYR* 3.1 57.7 + - + +
2367 LEU 3.1 21.7 + - - -
2387 LYS* 3.5 31.5 - - - +
2507 ILE* 3.6 25.4 - - + +
2517 GLY 3.1 26.7 - - - +
2527 ASN 3.5 0.9 - - - +
2537 GLU* 1.3 73.7 - - - +
2557 PHE* 1.4 59.6 + - + +
2587 PRO* 3.7 2.3 - - - +
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Residues in contact with PHE 255 (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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2187 TYR* 3.4 22.9 - - + +
2207 ALA* 4.4 3.4 - - + -
2237 PHE* 3.0 49.6 - + + -
2267 GLU* 3.4 55.4 - - + -
2277 MET* 3.3 35.7 - - + -
2307 ALA* 4.8 1.6 - - + -
2367 LEU* 4.5 9.6 - - + -
2517 GLY 5.1 1.1 - - - -
2527 ASN* 3.1 30.0 + - - -
2537 GLU 3.1 0.4 - - - -
2547 ARG* 1.4 79.3 - - + +
2567 ARG* 1.3 70.0 + - + +
2577 CYS 3.1 2.5 - - - -
2587 PRO* 3.6 1.4 - - - +
2597 GLU* 3.1 16.9 + - - +
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Residues in contact with ARG 256 (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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1887 TYR* 3.3 22.9 + - - +
1917 LYS* 5.9 0.2 - - - +
1927 ILE* 3.6 43.9 + - + +
1957 GLU* 3.7 13.9 + - - -
1967 ARG* 6.0 0.6 - - - +
2277 MET* 3.7 33.5 - - + +
2527 ASN* 3.8 9.2 - - - +
2537 GLU* 3.0 45.1 + - - +
2557 PHE* 1.3 85.3 - - + +
2577 CYS* 1.3 60.1 + - - +
2597 GLU* 4.0 7.6 - - - -
2607 THR* 3.4 2.1 + - - -
2667 PHE* 3.3 21.1 - - + -
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Residues in contact with CYS 257 (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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1857 LEU* 3.2 39.8 - - - +
1887 TYR* 3.8 9.4 - - - -
1897 LEU* 3.8 17.7 - - + -
1927 ILE* 4.0 7.8 - - + +
2137 LYS* 4.2 17.5 - - - -
2177 CYS* 4.2 8.7 - - - -
2537 GLU 3.1 14.2 + - - +
2557 PHE 3.1 0.8 - - - -
2567 ARG* 1.3 75.3 - - - +
2587 PRO* 1.3 69.4 - - + +
2607 THR* 2.6 27.5 + - - -
3067 TYR* 5.1 0.4 - - - -
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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