Contacts of the helix formed by residues 2520 - 2534 (chain B) in PDB entry 5WBY
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 ASP2520 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2408B ARG* 4.2 5.2 - - - +
2518B THR 3.7 3.8 + - - -
2519B LEU* 1.3 73.9 - - - +
2521B VAL* 1.3 60.2 + - - +
2522B PRO* 3.5 18.8 - - + +
2523B THR* 2.6 29.9 + - - -
2524B GLN* 3.0 25.6 + - - +
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Residues in contact with VAL2521 (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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2401B HIS* 3.7 31.2 - - + +
2404B MET* 4.0 14.1 - - + -
2405B GLU* 3.4 37.7 - - - +
2408B ARG* 3.5 38.3 - - - +
2520B ASP* 1.3 74.5 - - - +
2522B PRO* 1.4 67.1 - - + +
2524B GLN* 3.2 7.1 + - - +
2525B VAL* 2.8 31.5 + - + +
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Residues in contact with PRO2522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2397B ARG* 5.2 1.7 + - - -
2401B HIS* 3.5 33.9 + - + +
2405B GLU* 5.1 2.2 - - - +
2520B ASP* 3.5 18.2 - - + +
2521B VAL* 1.4 95.1 - - + +
2523B THR* 1.3 56.8 + - - +
2525B VAL* 4.1 0.5 - - - +
2526B GLU* 3.1 28.1 + - - +
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Residues in contact with THR2523 (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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2519B LEU* 3.7 27.4 - - + -
2520B ASP* 2.6 29.3 + - - -
2521B VAL 3.2 0.6 - - - -
2522B PRO* 1.3 74.2 - - - +
2524B GLN* 1.3 60.3 + - - +
2526B GLU* 3.3 7.5 + - + +
2527B LEU* 2.9 37.8 + - + +
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Residues in contact with GLN2524 (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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2332B TYR* 4.1 6.5 - - - -
2404B MET* 3.6 23.1 - - - +
2408B ARG* 3.2 28.4 + - - +
2507B LYS* 2.9 25.2 + - - +
2510B GLY* 4.3 1.0 - - - -
2512B ASP* 2.8 39.1 + - - +
2513B PHE* 4.3 5.6 - - + -
2519B LEU* 4.5 8.7 - - + +
2520B ASP 3.0 17.2 + - - +
2521B VAL* 3.6 3.6 - - - +
2523B THR* 1.3 76.7 - - - +
2525B VAL* 1.3 56.9 + - - +
2527B LEU* 3.3 11.4 + - - +
2528B LEU* 2.9 38.1 + - + +
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Residues in contact with VAL2525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2329B MET* 4.0 14.4 - - + -
2397B ARG* 4.1 7.0 - - + -
2400B CYS* 3.6 39.5 - - + +
2401B HIS* 3.8 24.9 - - + +
2404B MET* 4.4 6.3 - - + -
2521B VAL* 2.8 29.6 + - + +
2522B PRO 4.1 0.7 - - - +
2524B GLN* 1.3 71.8 - - + +
2526B GLU* 1.3 57.8 + - - +
2528B LEU* 3.3 8.9 + - + +
2529B ILE* 3.0 44.7 + - + +
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Residues in contact with GLU2526 (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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2397B ARG* 2.6 40.5 + - - +
2522B PRO 3.1 20.7 + - - +
2523B THR* 3.6 8.3 - - + +
2525B VAL* 1.3 77.2 - - - +
2527B LEU* 1.3 64.5 + - + +
2529B ILE* 3.4 4.8 + - - +
2530B LYS* 3.0 48.4 + - + +
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Residues in contact with LEU2527 (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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2513B PHE* 3.6 33.7 - - + -
2519B LEU* 3.6 40.8 - - + -
2523B THR* 2.9 30.6 + - + +
2524B GLN 3.5 4.5 - - - +
2526B GLU* 1.3 75.1 - - + +
2528B LEU* 1.3 56.3 + - - +
2530B LYS* 3.5 8.2 - - + +
2531B GLN* 3.1 26.2 + - - +
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Residues in contact with LEU2528 (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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2329B MET* 4.2 24.5 - - + -
2332B TYR* 3.5 58.3 - - + -
2376B PRO* 4.0 14.6 - - + +
2377B PHE* 4.0 12.3 - - + -
2404B MET* 4.4 3.8 - - + -
2513B PHE* 4.0 13.9 - - + -
2524B GLN* 2.9 31.3 + - + +
2525B VAL* 3.6 5.8 - - - +
2526B GLU 3.2 0.2 - - - -
2527B LEU* 1.3 74.5 - - - +
2529B ILE* 1.3 59.6 + - - +
2531B GLN* 3.1 8.7 + - - +
2532B ALA* 2.9 30.5 + - - +
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Residues in contact with ILE2529 (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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2329B MET* 5.7 0.4 - - + -
2377B PHE* 4.7 5.8 - - + -
2379B LEU* 3.8 19.7 - - + -
2392B LEU* 4.1 14.6 - - + +
2396B TYR* 4.0 28.9 - - + -
2397B ARG* 4.0 34.8 - - + +
2400B CYS* 5.3 0.7 - - - -
2525B VAL* 3.0 39.0 + - + +
2526B GLU* 3.4 5.8 + - - +
2528B LEU* 1.3 74.4 - - + +
2530B LYS* 1.3 59.3 + - - +
2532B ALA* 3.4 2.2 + - - +
2533B THR* 2.7 43.5 + - - +
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Residues in contact with LYS2530 (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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2526B GLU* 3.0 41.9 + - - +
2527B LEU* 3.5 10.3 - - + +
2529B ILE* 1.3 79.7 - - - +
2531B GLN* 1.3 56.7 + - - +
2533B THR* 3.8 7.6 - - - -
2534B SER* 3.0 30.1 + - - -
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Residues in contact with GLN2531 (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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2332B TYR* 5.3 2.7 + - - -
2366B MET* 4.1 15.6 - - - +
2374B LYS 3.5 15.7 + - - +
2375B ILE* 3.4 8.1 - - - +
2376B PRO* 3.8 22.1 - - + +
2513B PHE* 3.8 26.0 - - + -
2527B LEU 3.1 13.0 + - - +
2528B LEU* 3.1 12.6 + - - +
2530B LYS* 1.3 77.2 - - - +
2532B ALA* 1.3 59.7 + - - +
2533B THR 3.6 0.2 + - - -
2534B SER* 3.6 5.1 + - - -
2537B ASN* 2.8 38.3 + - - +
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Residues in contact with ALA2532 (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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2375B ILE* 3.7 19.8 - - - +
2376B PRO* 4.0 6.5 - - + +
2377B PHE* 3.5 33.2 - - + +
2379B LEU* 3.7 29.1 + - + +
2528B LEU 2.9 16.1 + - - +
2529B ILE 3.9 3.1 - - - +
2531B GLN* 1.3 77.2 - - - +
2533B THR* 1.3 59.7 + - - +
2534B SER 3.5 0.2 - - - -
2538B LEU* 3.9 12.0 - - - +
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Residues in contact with THR2533 (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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2379B LEU* 4.2 16.0 + - - +
2392B LEU* 5.0 9.6 - - + +
2529B ILE* 2.7 32.4 + - - +
2530B LYS* 4.0 9.2 - - - -
2532B ALA* 1.3 79.0 - - - +
2534B SER* 1.3 64.0 + - - +
2535B HIS* 3.2 11.4 + - + -
2538B LEU* 3.2 12.9 - - - +
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Residues in contact with SER2534 (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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2530B LYS 3.0 17.1 + - - -
2531B GLN* 4.6 0.4 - - - -
2532B ALA 3.5 1.8 - - - -
2533B THR* 1.3 74.1 - - - +
2535B HIS* 1.3 58.1 + - - +
2536B GLU* 3.3 22.9 + - - +
2537B ASN* 3.5 27.5 + - - +
2538B LEU* 2.9 30.5 + - - +
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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