Contacts of the helix formed by residues 252 - 257 (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 ASN 252 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1964 ARG* 3.5 19.1 + - - -
2274 MET* 5.7 1.6 - - - -
2304 ALA* 3.3 41.6 + - + +
2334 SER* 5.0 1.8 + - - -
2364 LEU* 3.9 12.2 - - - +
2374 GLU* 4.0 9.6 + - - +
2514 GLY* 1.3 74.4 - - - +
2534 GLU* 1.4 56.6 + - - +
2544 ARG* 2.8 16.6 + - - +
2554 PHE* 3.1 37.1 + - + -
2564 ARG* 3.8 13.0 - - - +
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Residues in contact with GLU 253 (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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1894 LEU* 4.6 5.0 - - + +
1924 ILE* 3.6 28.4 - - + +
1934 LEU* 4.1 17.3 - - + -
1964 ARG* 3.3 40.6 + - - +
2504 ILE* 3.5 12.9 - - + -
2514 GLY 3.0 28.4 + - - -
2524 ASN* 1.4 71.1 + - - +
2544 ARG* 1.3 64.5 + - - +
2554 PHE 3.1 0.9 - - - -
2564 ARG* 3.0 44.2 + - - +
2574 CYS* 3.1 18.0 + - - +
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Residues in contact with ARG 254 (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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1894 LEU* 5.7 0.4 - - - -
2154 LYS 5.4 0.2 + - - -
2164 LEU* 2.9 34.1 + - + +
2174 CYS* 2.9 30.1 - - - +
2184 TYR* 3.1 57.5 + - + +
2364 LEU 3.1 21.7 + - - -
2374 GLU 4.3 0.2 + - - -
2384 LYS* 3.5 31.3 - - - +
2504 ILE* 3.6 25.2 - - + +
2514 GLY 3.1 26.2 - - - +
2524 ASN 3.5 1.1 - - - +
2534 GLU* 1.3 75.0 - - - +
2554 PHE* 1.4 58.5 + - + +
2584 PRO* 3.7 1.6 - - - +
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Residues in contact with PHE 255 (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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2184 TYR* 3.4 23.8 - - + +
2204 ALA* 4.4 2.9 - - + -
2234 PHE* 3.0 51.1 - + + -
2264 GLU* 3.4 53.6 - - + -
2274 MET* 3.3 36.3 - - + -
2304 ALA* 4.8 1.8 - - + -
2364 LEU* 4.5 9.4 - - + -
2514 GLY 5.1 1.1 - - - -
2524 ASN* 3.1 30.0 + - - -
2534 GLU 3.1 0.4 - - - -
2544 ARG* 1.4 77.8 - - + +
2564 ARG* 1.3 70.7 + - + +
2574 CYS 3.1 2.2 - - - -
2584 PRO* 3.6 1.0 - - - +
2594 GLU* 3.1 16.2 + - - +
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Residues in contact with ARG 256 (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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1133 LYS* 6.1 1.2 - - - +
1884 TYR* 3.3 22.7 + - - +
1914 LYS* 5.9 0.2 - - - +
1924 ILE* 3.6 44.4 + - + +
1954 GLU* 3.7 14.1 + - - -
1964 ARG* 6.0 0.2 - - - +
2274 MET* 3.7 33.4 - - + +
2524 ASN* 3.8 10.1 - - - +
2534 GLU* 3.0 46.6 + - - +
2554 PHE* 1.3 84.0 - - + +
2574 CYS* 1.3 59.6 + - - +
2594 GLU* 4.0 7.6 - - - -
2604 THR* 3.4 2.4 + - - -
2664 PHE* 3.3 22.0 - - + -
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Residues in contact with CYS 257 (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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1854 LEU* 3.2 41.2 - - - +
1884 TYR* 3.8 9.9 - - - -
1894 LEU* 3.8 16.8 - - + -
1924 ILE* 4.0 7.8 - - + +
2134 LYS* 4.2 16.8 - - - -
2174 CYS* 4.2 10.1 - - - -
2534 GLU 3.1 12.9 + - - +
2554 PHE 3.1 0.6 - - - -
2564 ARG* 1.3 75.0 - - - +
2584 PRO* 1.3 70.2 - - + +
2604 THR* 2.6 27.5 + - - -
3064 TYR* 5.1 0.2 - - - -
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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