Contacts of the helix formed by residues 2262 - 2273 (chain N) 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 GLY2262 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755A GLU* 4.0 17.4 + - - -
758A THR* 6.6 0.2 - - - -
2261N LEU* 1.3 76.0 - - - +
2263N LEU* 1.3 68.5 + - - -
2264N GLU* 3.4 2.7 - - - -
2265N ASP* 3.0 14.8 + - - +
2266N ILE* 2.9 20.3 + - - +
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Residues in contact with LEU2263 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A 486 4.8 15.3 - - - -
571A VAL* 4.4 11.4 - - + -
600A TRP* 3.1 37.2 - - + +
755A GLU* 3.9 32.0 + - + +
756A ILE* 4.5 5.6 - - + -
758A THR* 5.8 2.6 - - - +
759A ASN* 3.1 26.7 - - + +
2262N GLY* 1.3 69.4 - - - -
2264N GLU* 1.3 56.6 + - - +
2266N ILE* 2.7 32.9 + - + +
2267N ILE* 3.0 37.6 + - + -
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Residues in contact with GLU2264 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A MET* 4.5 3.1 - - - +
597A GLN* 3.5 36.0 + - - +
758A THR* 4.7 18.4 - - + +
759A ASN* 4.3 7.0 - - + +
2262N GLY* 3.4 1.3 - - - -
2263N LEU* 1.3 83.6 - - - +
2265N ASP* 1.3 59.2 + - + +
2267N ILE* 3.9 5.9 - - - +
2268N ARG* 3.0 49.4 + - - +
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Residues in contact with ASP2265 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2260N ASN 4.9 2.4 - - - +
2261N LEU* 4.1 12.4 - - + -
2262N GLY* 3.0 29.1 + - - +
2263N LEU 3.0 0.4 - - - -
2264N GLU* 1.3 80.3 - - + +
2266N ILE* 1.3 56.6 + - - +
2268N ARG* 3.2 30.7 + - - +
2269N LYS* 2.8 49.1 + - - +
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Residues in contact with ILE2266 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A 486 5.5 8.5 - - - -
568A GLY* 4.5 17.7 - - - +
571A VAL* 4.3 17.7 - - + -
572A ILE* 3.6 33.4 - - + +
752A MET* 6.0 4.0 - - + -
755A GLU* 5.9 0.9 - - - +
529B THR* 5.5 6.5 - - - +
2261N LEU* 4.2 20.4 - - + +
2262N GLY 2.9 15.9 + - - +
2263N LEU* 2.7 19.7 + - + +
2265N ASP* 1.3 68.1 - - - +
2267N ILE* 1.3 60.0 + - - +
2269N LYS* 3.4 6.9 + - - +
2270N ALA* 2.8 29.3 + - - +
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Residues in contact with ILE2267 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A VAL* 4.0 14.1 - - + -
575A VAL* 4.1 14.4 - - + +
593A MET* 3.4 22.9 - - - -
596A LEU* 4.0 26.5 - - + +
597A GLN* 3.9 32.8 - - + +
600A TRP* 4.0 10.5 - - + -
759A ASN* 5.1 0.2 - - + -
2263N LEU* 3.0 37.9 + - + +
2264N GLU* 3.9 9.6 - - - +
2266N ILE* 1.3 75.4 - - - +
2268N ARG* 1.3 57.8 + - - +
2270N ALA* 3.3 2.1 + - - +
2271N LEU* 2.9 28.6 + - - +
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Residues in contact with ARG2268 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A MET* 3.5 26.1 - - + +
2264N GLU* 3.0 49.9 + - - +
2265N ASP* 3.2 31.2 + - - +
2267N ILE* 1.3 77.1 - - - +
2269N LYS* 1.3 66.0 + - - +
2271N LEU* 3.1 13.5 + - - +
2272N MET* 3.2 22.6 + - + +
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Residues in contact with LYS2269 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2260N ASN 5.9 0.7 - - - -
2261N LEU* 4.8 17.5 - - + -
2265N ASP* 2.8 38.3 + - - +
2266N ILE* 3.7 6.7 - - - +
2268N ARG* 1.3 76.1 - - - +
2270N ALA* 1.3 56.8 + - - +
2272N MET* 5.1 1.1 - - - -
2273N GLY* 2.6 44.0 + - - +
2274N SER* 3.5 34.5 + - - +
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Residues in contact with ALA2270 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ILE* 4.3 25.8 - - + +
575A VAL* 3.5 29.3 - - + +
576A LYS* 5.2 4.1 - - + +
579A LYS* 3.4 12.5 + - - -
542B GLU* 3.8 7.8 - - - +
2266N ILE 2.8 21.3 + - - +
2267N ILE 3.7 1.3 - - - +
2269N LYS* 1.3 69.9 - - - +
2271N LEU* 1.3 66.3 + - - +
2272N MET* 3.0 6.1 + - - -
2273N GLY* 4.2 0.3 + - - -
2274N SER* 4.5 7.3 + - - +
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Residues in contact with LEU2271 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A VAL* 3.6 2.8 - - + +
579A LYS* 2.7 53.2 + - + +
589A LEU* 3.9 26.9 - - + +
592A GLN* 3.7 15.3 - - + +
593A MET* 3.5 44.0 - - + +
596A LEU* 3.7 24.2 - - + -
2267N ILE* 2.9 17.6 + - + +
2268N ARG 3.1 6.5 + - - +
2270N ALA* 1.3 76.5 - - - +
2272N MET* 1.3 66.1 + - - +
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Residues in contact with MET2272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A LYS* 4.3 6.1 + - - +
589A LEU* 5.0 22.0 - - + -
593A MET* 5.5 2.7 - - + -
542B GLU* 5.2 1.4 - - - +
576C LYS* 4.6 8.3 + - - -
2268N ARG* 3.2 25.1 + - + +
2269N LYS* 3.4 2.2 - - - +
2270N ALA 3.0 4.8 - - - -
2271N LEU* 1.3 93.8 - - + +
2273N GLY* 1.3 58.3 + - - +
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Residues in contact with GLY2273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C LYS* 4.1 21.1 - - - -
2269N LYS* 2.6 20.3 + - - +
2270N ALA 4.2 0.6 + - - -
2272N MET* 1.3 78.3 - - - +
2274N SER* 1.3 67.5 + - - +
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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