Contacts of the strand formed by residues 2452 - 2457 (chain G) in PDB entry 2ZLE
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 TYR2452 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1932F MET* 4.7 5.4 - - + +
1933F PRO* 3.3 42.8 + - + +
1934F SER* 4.0 7.0 - - - -
1935F LEU* 3.7 27.0 - - + +
2072F SER* 5.2 3.6 - - - -
2451G ASP* 1.3 77.9 - - - +
2453G THR* 1.3 61.0 + - - +
2469G GLY 3.4 15.0 - - - +
2470G ILE* 3.4 19.3 - - + -
2471G VAL* 5.1 0.2 - - - +
2497G ASN* 4.0 19.6 - - - +
2498G LEU* 3.6 37.4 + - + -
2503G ILE* 4.8 1.7 - - - +
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Residues in contact with THR2453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2452G TYR* 1.3 75.3 + - - +
2454G VAL* 1.3 63.5 + - - +
2468G SER* 3.5 3.3 - - - -
2469G GLY 2.8 34.2 + - - +
2470G ILE* 3.9 11.2 - - - +
2471G VAL* 3.8 12.0 - - - +
2482G THR* 3.0 27.8 + - - +
2484G ALA* 3.5 13.7 - - + -
2495G LEU* 3.4 20.5 - - + +
2496G VAL 3.8 3.1 - - - -
2497G ASN* 5.1 0.4 - - - +
2498G LEU* 5.6 3.2 - - - +
2503G ILE* 3.5 23.7 - - - +
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Residues in contact with VAL2454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2331G LEU* 4.9 7.0 - - + -
2334G MET* 3.2 18.4 - - + -
2335G LEU* 4.3 12.6 - - + -
2453G THR* 1.3 75.6 - - - +
2455G ALA* 1.3 64.7 + - - +
2456G ILE* 4.7 3.3 - - + +
2466G VAL* 3.7 23.8 - - + -
2467G THR 3.5 13.2 - - - +
2468G SER* 4.7 7.2 - - - -
2494G ALA 3.8 0.5 - - - +
2495G LEU* 3.5 4.0 - - - +
2496G VAL* 2.8 73.7 + - + +
2497G ASN 4.1 1.8 - - - +
2498G LEU* 5.5 3.4 - - + -
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Residues in contact with ALA2455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2454G VAL* 1.3 70.8 - - - +
2456G ILE* 1.3 65.6 + - - +
2457G GLY 4.3 0.2 - - - -
2465G THR 3.9 0.5 - - - +
2466G VAL* 3.2 5.0 - - - +
2467G THR* 2.8 42.7 + - + +
2484G ALA* 3.6 25.2 - - + +
2494G ALA 3.2 8.1 - - - +
2495G LEU* 4.1 6.0 - - + +
2506G ASN* 3.9 13.7 - - - +
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Residues in contact with ILE2456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2335G LEU* 4.5 11.9 - - + -
2338G VAL* 3.7 29.6 - - + -
2339G MET* 4.0 28.0 - - + -
2342G VAL* 4.0 29.4 - - + +
2378G SER* 4.6 3.0 - - - -
2454G VAL* 4.7 7.2 - - + +
2455G ALA* 1.3 83.4 - - - +
2457G GLY* 1.3 62.2 + - - +
2464G GLU* 5.1 4.3 - - + +
2465G THR 3.5 9.0 - - - +
2466G VAL* 4.3 11.2 - - + -
2492G GLY* 5.4 0.2 - - - -
2493G GLY* 3.5 5.0 + - - -
2494G ALA* 2.9 37.3 + - + +
2496G VAL* 5.0 9.2 - - + -
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Residues in contact with GLY2457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2378G SER* 3.5 13.9 - - - -
2456G ILE* 1.3 77.1 - - - +
2458G ASN* 1.3 59.8 + - - -
2459G PRO* 3.1 10.1 - - - +
2464G GLU* 3.4 6.0 - - - -
2465G THR 2.8 32.6 + - - +
2492G GLY* 4.2 15.3 - - - -
2493G GLY 4.2 0.2 - - - -
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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