Contacts of the helix formed by residues 2361 - 2366 (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 ILE2361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2243B TYR* 3.2 42.4 - - + -
2244B PRO 3.6 9.9 - - - +
2245B VAL* 6.2 0.2 - - + -
2246B PHE* 4.1 4.5 - - - -
2306B SER* 5.5 6.1 - - - +
2310B PHE* 5.9 1.6 - - + -
2311B VAL* 4.0 16.6 - - + -
2314B TRP* 4.3 25.5 - - + +
2315B LEU* 5.3 3.4 - - + -
2359B GLU 5.6 0.4 - - - +
2360B LEU* 1.3 82.0 - - - +
2362B PRO* 1.3 67.0 - - + +
2363B GLU* 2.8 31.4 - - + +
2364B PHE* 3.0 32.6 + - + +
2365B TYR* 4.2 4.9 - - - -
2370B MET* 5.1 2.0 - - + -
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Residues in contact with PRO2362 (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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2223B PHE* 4.0 1.8 - - + -
2227B MET* 4.1 6.1 - - - -
2237B TYR* 3.9 18.8 - - + +
2243B TYR* 4.3 2.2 - - + -
2244B PRO* 3.5 36.3 - - + +
2246B PHE* 3.6 35.5 - - + -
2361B ILE* 1.3 89.8 - - + +
2363B GLU* 1.3 69.1 + - - +
2365B TYR* 2.8 25.1 + - - +
2366B TYR* 3.3 19.1 - - + -
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Residues in contact with GLU2363 (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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2237B TYR* 3.5 11.1 - - - -
2243B TYR* 2.5 27.9 + - - -
2315B LEU* 4.2 11.1 - - + +
2361B ILE* 2.8 24.2 + - + +
2362B PRO* 1.3 85.5 - - - +
2364B PHE* 1.3 59.0 + - - +
2365B TYR 2.9 0.4 - - - -
2366B TYR* 3.6 23.5 + - - +
2367B LEU* 2.8 45.0 + - + +
2370B MET* 2.8 33.3 - - + +
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Residues in contact with PHE2364 (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* 4.8 10.1 - + - -
2314B TRP* 3.4 51.1 - + - -
2340B PHE* 4.2 4.0 - + - -
2343B ILE* 4.6 6.1 - - + -
2346B ALA* 6.1 0.2 - - + -
2360B LEU* 3.9 30.1 - - + -
2361B ILE* 3.0 21.4 + - + +
2362B PRO 3.0 0.4 + - - -
2363B GLU* 1.3 77.2 - - - +
2365B TYR* 1.3 67.4 + - + +
2366B TYR 3.8 0.3 + - - -
2370B MET* 3.4 19.5 - - - +
2371B PHE* 3.9 30.2 - + - -
2403B PHE* 4.1 19.1 - + - -
2404B VAL* 4.0 10.1 - - - +
2407B ASN* 3.0 30.0 + - - +
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Residues in contact with TYR2365 (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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2223B PHE* 4.1 16.3 - - + -
2246B PHE* 3.7 31.6 - + + -
2247B PRO 2.6 29.2 + - - -
2249B VAL* 3.3 25.4 + - + +
2250B ILE* 6.2 0.9 - - + -
2360B LEU* 3.7 11.2 - - + +
2361B ILE 4.2 3.1 - - - -
2362B PRO 2.8 12.5 + - - +
2364B PHE* 1.3 87.9 - - + +
2366B TYR* 1.3 63.4 + - - +
2404B VAL* 3.5 8.2 - - - +
2407B ASN* 3.3 46.0 - - + -
2408B ARG* 3.8 24.2 + - - +
2411B LEU* 3.7 23.8 - - + -
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Residues in contact with TYR2366 (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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2223B PHE* 3.7 26.0 - + + -
2237B TYR* 4.1 11.6 + - - -
2362B PRO* 3.3 34.3 - - + -
2363B GLU* 3.1 32.9 + - + +
2365B TYR* 1.3 79.7 - - - +
2367B LEU* 1.3 78.2 + - + +
2368B PRO* 3.2 9.9 - - - +
2404B VAL* 3.2 17.3 - - - +
2408B ARG* 6.2 1.3 - - - +
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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