Contacts of the strand formed by residues 2342 - 2353 (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 VAL2342 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2338G VAL* 4.6 10.1 - - + -
2339G MET* 2.9 24.2 + - + +
2340G PRO 4.6 0.7 - - - +
2341G SER* 1.3 81.5 - - - +
2343G VAL* 1.3 67.2 + - - +
2378G SER* 4.6 7.2 - - - -
2379G GLY 3.6 8.3 - - - +
2380G VAL* 4.5 14.8 - - + -
2407G SER* 4.0 16.5 + - - -
2439G ILE* 5.9 1.3 - - + -
2456G ILE* 4.0 44.6 - - + +
2464G GLU* 3.3 27.2 - - + +
2494G ALA* 4.6 4.5 - - + +
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Residues in contact with VAL2343 (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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2341G SER 4.0 0.9 - - - +
2342G VAL* 1.3 78.8 - - - +
2344G SER* 1.3 71.0 + - - +
2345G ILE* 3.9 13.2 - - + -
2378G SER* 3.5 1.9 - - - -
2379G GLY 3.0 31.9 + - - +
2381G ILE* 3.6 36.3 - - + -
2389G VAL* 4.1 15.7 - - + -
2404G VAL* 3.5 22.7 - - + -
2405G GLN 3.7 8.5 - - - +
2406G LEU* 3.9 12.8 - - + +
2430G ILE* 5.2 0.2 - - + -
2464G GLU* 3.3 12.8 - - - +
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Residues in contact with SER2344 (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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2343G VAL* 1.3 76.8 - - - +
2345G ILE* 1.3 68.3 + - - +
2346G ASN* 5.4 4.5 - - - -
2377G GLY 3.8 5.4 - - - -
2404G VAL* 3.4 3.8 - - - -
2405G GLN* 3.1 46.9 + - - +
2406G LEU 5.1 1.0 + - - -
2407G SER* 6.1 0.3 - - - -
2458G ASN* 5.4 5.2 - - - -
2464G GLU* 3.8 25.2 - - - +
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Residues in contact with ILE2345 (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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2343G VAL* 3.9 10.3 - - + -
2344G SER* 1.3 81.7 - - - +
2346G ASN* 1.3 68.5 + - - +
2347G VAL* 3.7 19.1 - - + -
2376G LEU* 3.1 7.3 - - - +
2377G GLY 2.9 39.8 + - - +
2378G SER 3.8 9.2 - - - +
2379G GLY* 4.0 5.2 - - - -
2389G VAL* 4.5 1.1 - - + -
2391G THR* 3.6 40.6 - - + +
2395G VAL* 4.4 6.3 - - + -
2396G VAL* 4.8 2.2 - - + -
2402G ILE* 3.6 21.1 - - + -
2403G LYS 3.3 3.4 - - - -
2404G VAL* 4.2 6.7 - - + -
2428G ILE* 3.9 14.6 - - + -
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Residues in contact with ASN2346 (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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2344G SER* 5.4 4.0 - - - -
2345G ILE* 1.3 78.1 + - - +
2347G VAL* 1.3 65.3 + - - +
2374G MET* 6.0 5.5 - - - +
2375G ALA 3.6 4.9 + - - -
2376G LEU* 4.1 19.6 - - - +
2401G VAL* 3.8 1.2 - - - +
2402G ILE* 3.6 0.7 - - - -
2403G LYS* 2.7 51.5 + - + +
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Residues in contact with VAL2347 (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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2345G ILE* 3.7 20.2 - - + -
2346G ASN* 1.3 80.9 + - - +
2348G GLU* 1.3 68.1 + - - +
2373G PHE* 4.5 9.0 - - + -
2374G MET* 3.4 7.1 - - - +
2375G ALA* 2.8 35.1 + - + +
2395G VAL* 3.5 31.4 - - + +
2396G VAL* 4.0 13.0 - - + -
2399G ALA* 3.3 34.8 - - + +
2401G VAL 3.4 2.7 - - - +
2402G ILE* 4.3 7.0 - - + -
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Residues in contact with GLU2348 (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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2346G ASN 5.5 0.2 - - - +
2347G VAL* 1.3 78.5 - - - +
2349G GLY* 1.3 61.7 + - - +
2372G LYS* 5.2 17.3 + - + +
2373G PHE 3.7 8.7 - - - +
2374G MET* 4.8 7.9 - - + +
2399G ALA* 3.7 1.4 - - - -
2400G THR* 2.8 6.6 + - - +
2401G VAL* 2.8 57.8 + - + +
2403G LYS* 5.9 1.2 + - - +
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Residues in contact with GLY2349 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2348G GLU* 1.3 78.6 - - - +
2350G SER* 1.3 61.4 + - - -
2372G LYS* 3.3 6.5 - - - +
2373G PHE* 2.8 43.7 + - - -
2398G ASN 3.6 11.4 - - - -
2400G THR* 3.4 15.7 - - - -
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Residues in contact with SER2350 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2349G GLY* 1.3 76.0 - - - -
2351G THR* 1.3 69.0 + - - +
2370G GLN* 3.4 23.3 + - - +
2371G GLN 3.0 21.5 - - - -
2372G LYS* 4.1 8.3 - - - -
2373G PHE* 3.3 8.2 - - - -
2398G ASN* 3.7 18.9 + - - +
2400G THR* 3.7 8.4 + - - -
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Residues in contact with THR2351 (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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2350G SER* 1.3 82.5 + - - +
2352G THR* 1.3 76.6 + - - +
2353G VAL* 3.7 2.4 + - + +
2370G GLN* 3.0 14.8 - - - +
2371G GLN* 2.7 40.7 + - + +
2373G PHE* 4.0 17.3 - - + -
2398G ASN* 4.9 13.2 + - - -
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Residues in contact with THR2352 (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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2351G THR* 1.3 83.6 + - - +
2353G VAL* 1.3 71.8 + - - +
2354G ASN* 5.7 2.2 - - - +
2368G GLY* 4.7 6.3 - - - -
2369G GLN 3.7 8.4 + - - +
2370G GLN* 2.4 21.6 + - - +
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Residues in contact with VAL2353 (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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2351G THR* 5.7 2.2 - - + -
2352G THR* 1.3 77.1 - - - +
2354G ASN* 1.3 76.7 + - + +
2356G PRO* 6.2 0.4 - - + -
2368G GLY* 3.6 4.9 - - - -
2369G GLN* 3.1 35.3 + - + +
2371G GLN* 3.0 46.4 - - + +
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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