Contacts of the helix formed by residues 2272 - 2277 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2267C ARG* 4.1 3.4 - - - +
2270C SER 4.4 0.2 - - - +
2271C LYS* 1.3 89.3 - - + +
2273C ILE* 1.3 69.1 + - - +
2274C GLY 4.4 2.5 - - - +
2275C ALA* 2.9 20.8 + - + -
2276C LEU* 3.5 7.7 + - - +
2301C TYR* 4.1 6.3 - - + +
2359C GLU* 5.0 1.3 - - - +
2423C TRP* 6.1 0.2 - - + -
2426C LEU* 3.5 18.4 - - + -
2427C ILE* 6.5 0.7 - - + -
2440C ALA* 3.3 19.3 - - + +
2441C LEU 3.2 25.8 - - - +
2442C ASN* 3.4 21.1 - - - +
2444C PHE* 5.4 4.5 - - + -
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Residues in contact with ILE2273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248C TRP* 3.6 26.5 - - + -
2267C ARG* 3.4 24.9 - - - +
2272C PRO* 1.3 71.5 - - - +
2274C GLY* 1.3 59.7 + - - +
2275C ALA 2.9 6.8 + - - -
2276C LEU* 3.0 30.0 + - + +
2280C ARG* 3.3 8.2 + - - +
2347C TRP* 4.8 3.4 - - + -
2350C SER* 3.3 29.8 - - - +
2351C GLN* 4.9 3.8 - - - +
2357C ILE* 3.5 33.2 - - + +
2358C LYS 3.7 7.6 - - - +
2359C GLU* 3.6 19.4 + - + +
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Residues in contact with GLY2274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2272C PRO* 3.2 2.0 + - - +
2273C ILE* 1.3 76.9 - - - +
2275C ALA* 1.3 57.6 + - - +
2276C LEU 3.9 0.2 + - - -
2277C ASN 4.3 1.0 - - - +
2280C ARG* 3.9 7.1 + - - -
2281C ALA* 3.7 11.6 + - - +
2284C PHE* 3.4 21.5 - - - -
2301C TYR* 3.4 24.3 + - - -
2357C ILE* 3.3 27.6 - - - +
2441C LEU* 4.3 0.2 - - - -
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Residues in contact with ALA2275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2271C LYS* 3.8 25.2 - - + -
2272C PRO* 2.9 28.8 + - + +
2274C GLY* 1.3 76.6 - - - +
2276C LEU* 1.3 68.1 + - - +
2277C ASN 3.3 5.7 + - - -
2278C PRO* 4.5 1.9 - - - +
2281C ALA* 4.1 7.8 - - + +
2301C TYR* 3.9 1.0 + - - -
2440C ALA 4.3 1.1 - - - +
2441C LEU* 3.7 26.0 - - + -
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Residues in contact with LEU2276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251C THR* 5.5 0.4 - - + -
2267C ARG* 3.8 19.7 - - + +
2268C ASP* 3.9 21.3 - - + +
2271C LYS* 3.8 32.8 - - + +
2272C PRO 3.7 5.2 - - - +
2273C ILE* 3.0 25.1 + - + +
2275C ALA* 1.3 79.6 - - - +
2277C ASN* 1.3 57.3 + - - +
2278C PRO* 3.2 12.8 - - - +
2347C TRP* 3.8 28.0 - - + -
2351C GLN* 3.3 20.2 - - - +
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Residues in contact with ASN2277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2273C ILE 4.3 1.6 + - - -
2274C GLY 4.3 1.7 + - - +
2275C ALA* 3.3 0.4 - - - +
2276C LEU* 1.3 78.5 - - - +
2278C PRO* 1.3 56.5 - - - +
2279C LYS* 2.7 26.7 + - - +
2280C ARG* 3.0 19.3 + - + +
2281C ALA* 2.7 37.0 + - - +
2351C GLN* 3.1 43.5 + - - +
2352C ARG* 4.4 10.9 - - - +
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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