Contacts of the helix formed by residues 2265 - 2272 (chain M) in PDB entry 3H52
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 ASP2265 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593B MET* 4.3 7.7 - - - +
597B GLN* 5.5 1.2 + - - -
755B GLU* 3.7 42.9 + - + +
756B ILE* 4.2 16.5 - - + +
759B ASN* 3.2 23.9 + - - +
2266M ILE* 1.3 57.8 + - - +
2267M ILE* 3.0 18.2 + - - +
2268M ARG* 3.0 28.8 + - - +
2269M LYS* 2.6 39.3 + - - +
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Residues in contact with ILE2266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 486 6.6 0.2 - - - -
568B GLY* 5.2 7.2 - - - +
571B VAL* 4.9 7.2 - - + -
572B ILE* 4.2 21.7 - - + +
575B VAL* 5.1 0.2 - - - +
752B MET* 5.6 13.5 - - + +
755B GLU* 4.9 1.2 + - - -
756B ILE* 4.4 19.3 - - + +
2265M ASP* 1.3 74.5 + - - +
2267M ILE* 1.3 57.1 + - - +
2269M LYS* 3.6 10.7 - - - +
2270M ALA* 2.9 28.9 + - - +
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Residues in contact with ILE2267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B VAL* 3.8 22.7 - - + -
575B VAL* 3.8 21.0 - - + +
593B MET* 3.7 21.3 - - + -
596B LEU* 4.0 23.6 - - + +
597B GLN* 4.4 10.3 - - + -
600B TRP* 4.0 28.0 - - + -
756B ILE* 4.0 23.1 - - + -
2265M ASP* 3.1 8.6 + - - +
2266M ILE* 1.3 75.5 - - - +
2268M ARG* 1.3 56.1 + - - +
2269M LYS 3.3 0.2 - - - -
2270M ALA* 3.8 0.5 - - - +
2271M LEU* 2.7 36.6 + - - +
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Residues in contact with ARG2268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B LEU* 3.9 16.2 - - - +
590B ASP* 3.4 28.5 + - - +
593B MET* 3.6 40.8 - - + +
2265M ASP* 3.0 26.6 + - - +
2267M ILE* 1.3 74.5 - - - +
2269M LYS* 1.3 65.1 - - - +
2271M LEU* 4.5 2.9 - - - +
2272M MET* 3.1 49.0 + - + +
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Residues in contact with LYS2269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ILE* 4.5 26.2 - - - +
2265M ASP 2.6 25.2 + - - +
2266M ILE* 3.6 11.2 - - - +
2268M ARG* 1.3 74.7 - - - +
2270M ALA* 1.3 64.1 + - - +
2272M MET* 3.8 1.3 - - - -
2273M GLY 3.4 4.2 + - - +
2274M SER* 3.2 67.0 + - - +
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Residues in contact with ALA2270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ILE* 3.9 26.9 - - + +
575B VAL* 3.6 29.3 - - + +
576B LYS* 5.1 6.2 - - + +
579B LYS* 3.4 12.3 + - - -
2266M ILE 2.9 21.0 + - - +
2267M ILE 3.8 1.8 - - - +
2268M ARG 3.3 0.2 - - - -
2269M LYS* 1.3 77.1 - - - +
2271M LEU* 1.3 66.7 + - - +
2273M GLY* 3.9 6.2 + - - +
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Residues in contact with LEU2271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B VAL* 3.6 8.7 - - + +
579B LYS* 2.7 33.6 + - + +
589B LEU* 3.9 32.0 - - + +
592B GLN* 3.9 20.0 - - + +
593B MET* 3.2 53.4 - - + +
596B LEU* 4.1 13.2 - - + -
2267M ILE 2.7 21.4 + - - +
2268M ARG* 4.1 5.6 - - - +
2269M LYS 3.4 0.2 - - - -
2270M ALA* 1.3 73.4 - - - +
2272M MET* 1.3 59.2 + - + +
2273M GLY 3.4 0.3 + - - -
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Residues in contact with MET2272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B LEU* 4.8 18.4 - - + -
2268M ARG* 3.1 33.1 + - + +
2269M LYS* 3.8 2.0 - - - +
2271M LEU* 1.3 77.9 - - + +
2273M GLY* 1.3 49.4 + - - +
2274M SER 2.6 40.0 + - - +
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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