Contacts of the helix formed by residues 2272 - 2276 (chain B) in PDB entry 1T77
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 PRO2272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2267B ARG* 4.0 3.1 - - - +
2270B SER 4.4 0.4 - - - +
2271B LYS* 1.3 91.7 - - + +
2273B ILE* 1.3 68.0 + - - +
2274B GLY 4.3 0.9 - - - +
2275B ALA* 3.0 18.6 + - + +
2276B LEU* 3.6 8.2 + - - +
2301B TYR* 4.3 8.7 - - + +
2359B GLU* 5.0 1.1 - - - +
2426B LEU* 3.5 15.9 - - + -
2440B ALA* 3.3 28.3 - - + +
2441B LEU 3.5 11.2 - - - +
2442B ASN* 3.2 32.3 - - + +
2444B PHE* 5.5 3.4 - - + -
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Residues in contact with ILE2273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248B TRP* 3.5 25.6 - - + -
2267B ARG* 3.3 25.9 - - - +
2272B PRO* 1.3 70.9 - - - +
2274B GLY* 1.3 64.7 + - - +
2276B LEU* 3.0 31.8 + - + +
2280B ARG* 3.3 6.5 + - - +
2347B TRP* 4.8 1.1 - - + -
2350B SER* 3.5 26.9 - - - +
2351B GLN* 4.4 6.5 + - - +
2357B ILE* 3.5 32.8 - - + +
2358B LYS 4.1 5.8 - - - +
2359B GLU* 3.3 25.0 + - + +
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Residues in contact with GLY2274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2272B PRO* 3.3 2.0 - - - +
2273B ILE* 1.3 78.0 - - - +
2275B ALA* 1.3 59.1 + - - +
2276B LEU 3.7 0.3 + - - -
2277B ASN 4.2 1.4 - - - +
2280B ARG* 3.6 8.3 + - - -
2281B ALA* 3.8 10.6 + - - +
2284B PHE* 3.6 18.7 - - - -
2301B TYR* 3.7 24.1 + - - -
2357B ILE* 3.5 24.6 - - - +
2441B LEU* 4.4 0.2 - - - -
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Residues in contact with ALA2275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2271B LYS* 4.0 27.9 + - + +
2272B PRO* 3.0 29.4 + - + +
2274B GLY* 1.3 76.7 - - - +
2276B LEU* 1.3 65.4 + - - +
2277B ASN 3.5 1.4 - - - -
2278B PRO* 4.7 1.2 - - - +
2281B ALA* 4.1 16.3 - - + +
2301B TYR* 4.0 1.6 + - - -
2440B ALA 4.4 0.7 - - - +
2441B LEU* 4.1 22.7 - - + -
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Residues in contact with LEU2276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251B THR* 5.7 0.4 - - + -
2267B ARG* 3.9 17.3 - - + +
2268B ASP* 4.0 18.4 - - + +
2271B LYS* 3.7 28.0 - - + +
2272B PRO 3.6 13.0 - - - +
2273B ILE* 3.0 27.7 + - + +
2275B ALA* 1.3 79.4 - - - +
2277B ASN* 1.3 56.9 + - - +
2278B PRO* 3.3 12.0 - - - +
2347B TRP* 3.8 28.9 - - + -
2351B GLN* 3.9 16.8 - - - +
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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