Contacts of the helix formed by residues 2262 - 2266 (chain A) 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 LEU2262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2252A ASN* 6.0 0.2 - - - +
2259A ASP* 3.3 33.5 + - + +
2260A LEU 3.5 0.2 - - - -
2261A THR* 1.3 76.1 + - - +
2263A PRO* 1.3 79.3 - - + +
2264A THR* 3.7 22.7 - - + -
2265A ASN* 2.9 28.0 + - - +
2266A PHE* 3.2 13.3 - - - -
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Residues in contact with PRO2263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2261A THR 3.2 9.1 - - - +
2262A LEU* 1.3 90.0 - - + +
2264A THR* 1.3 56.3 + - - +
2266A PHE* 3.0 28.9 + - + +
2415A PHE* 3.8 29.2 - - + -
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Residues in contact with THR2264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251A THR* 3.7 8.7 + - - -
2252A ASN* 5.5 0.3 - - - +
2262A LEU* 2.9 31.8 + - + -
2263A PRO* 1.3 80.0 - - - +
2265A ASN* 1.3 68.2 + - - +
2266A PHE 3.3 3.9 + - - +
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Residues in contact with ASN2265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2250A ILE* 3.6 8.3 - - - +
2251A THR* 3.0 28.5 + - - -
2252A ASN* 2.6 38.2 + - - +
2257A GLU 5.4 0.4 + - - -
2258A LEU* 3.8 15.0 - - + +
2259A ASP 3.0 37.7 + - - +
2262A LEU* 2.9 26.9 + - - +
2264A THR* 1.3 86.9 - - - +
2266A PHE* 1.3 65.8 + - + +
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Residues in contact with PHE2266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2249A VAL* 3.5 29.4 - - + -
2250A ILE* 5.7 2.7 - - + -
2251A THR* 3.7 7.0 + - - +
2260A LEU* 3.6 46.7 - - + -
2262A LEU 3.2 20.9 - - - -
2263A PRO* 3.0 16.4 + - + +
2264A THR 4.7 1.9 - - - +
2265A ASN* 1.3 87.6 - - + +
2267A ARG* 1.3 67.0 + - - +
2268A ASP* 3.6 2.3 + - - +
2410A ALA* 4.2 8.1 - - + -
2413A SER* 3.5 22.4 - - - -
2415A PHE* 3.6 32.3 - + + -
2416A VAL* 4.5 2.9 - - + -
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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