Contacts of the helix formed by residues 2493 - 2510 (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 LEU2493 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2428B ASN* 4.4 31.8 - - + +
2429B TRP* 5.9 0.4 - - - -
2431B LEU* 4.3 9.8 - - + +
2432B MET* 4.1 41.3 - - + +
2492B ALA* 1.3 76.0 - - + +
2494B ASN* 1.3 56.1 + - - +
2495B LYS 3.2 2.2 - - - -
2496B LYS* 3.1 24.3 + - + +
2497B ALA* 2.8 36.3 + - - +
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Residues in contact with ASN2494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809B GLN* 5.5 6.9 - - - +
2423B TYR* 4.3 13.4 - - - -
2492B ALA 3.8 11.0 - - - +
2493B LEU* 1.3 77.7 - - - +
2495B LYS* 1.3 59.2 + - - +
2497B ALA* 3.7 6.0 + - - +
2498B ILE* 3.2 36.4 + - - +
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Residues in contact with LYS2495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2492B ALA* 3.6 16.3 + - - +
2493B LEU 3.2 0.6 - - - -
2494B ASN* 1.3 76.5 - - - +
2496B LYS* 1.3 63.7 + - - +
2498B ILE* 3.3 20.0 + - + +
2499B GLN* 3.3 39.7 + - + +
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Residues in contact with LYS2496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2367B THR* 5.4 10.9 + - - +
2431B LEU* 4.3 18.8 - - + +
2434B THR* 4.3 19.1 + - - +
2492B ALA 3.8 3.7 + - - +
2493B LEU* 3.1 32.7 + - + +
2495B LYS* 1.3 76.4 - - - +
2497B ALA* 1.3 64.7 + - - +
2499B GLN* 3.3 38.3 + - - +
2500B ILE* 3.4 33.7 + - + +
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Residues in contact with ALA2497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2422B VAL* 3.7 21.2 - - + +
2423B TYR* 3.5 29.2 - - + -
2428B ASN* 5.2 4.0 - - - +
2431B LEU* 4.8 5.3 - - + +
2493B LEU 2.8 20.2 + - - +
2494B ASN* 3.7 4.7 - - - +
2496B LYS* 1.3 73.4 - - - +
2498B ILE* 1.3 62.1 + - - +
2500B ILE* 3.4 8.0 + - - +
2501B ILE* 3.3 29.2 + - - +
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Residues in contact with ILE2498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1806B HIS* 6.1 5.8 - - + -
1809B GLN* 5.5 8.1 - - - +
2423B TYR* 3.6 19.3 - - - +
2494B ASN* 3.2 34.7 + - - +
2495B LYS* 3.3 13.4 + - + +
2496B LYS 3.3 0.8 - - - -
2497B ALA* 1.3 77.6 - - - +
2499B GLN* 1.3 61.7 + - - +
2501B ILE* 3.5 3.1 + - - +
2502B ASN* 2.9 47.7 + - - +
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Residues in contact with GLN2499 (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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2495B LYS* 3.3 45.2 + - + +
2496B LYS* 3.3 37.7 + - + +
2497B ALA 3.3 0.6 - - - -
2498B ILE* 1.3 78.4 - - + +
2500B ILE* 1.3 56.3 - - - +
2502B ASN* 3.5 8.5 + - - +
2503B ARG* 2.9 29.2 + - - +
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Residues in contact with ILE2500 (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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2362B PHE* 3.3 46.7 - - + -
2363B GLU 5.9 0.7 - - - +
2422B VAL* 4.3 8.7 - - + -
2431B LEU* 3.4 44.6 - - + -
2496B LYS* 3.4 39.0 - - - +
2497B ALA* 3.4 7.1 + - - +
2498B ILE 3.3 0.4 - - - -
2499B GLN* 1.3 75.8 - - + +
2501B ILE* 1.3 59.6 + - - +
2503B ARG* 3.0 10.8 + - + +
2504B VAL* 2.9 26.7 + - + +
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Residues in contact with ILE2501 (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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2415B MET* 3.7 12.8 - - + +
2418B LEU* 5.4 1.3 - - + -
2419B GLU* 3.7 28.9 - - + +
2422B VAL* 3.6 29.4 - - + -
2423B TYR* 3.2 45.5 - - + +
2497B ALA 3.3 15.5 + - - +
2498B ILE* 4.1 3.6 - - - +
2500B ILE* 1.3 72.3 - - + +
2502B ASN* 1.3 61.2 + - - +
2504B VAL* 3.3 9.8 + - + +
2505B ARG* 3.0 41.9 + - - +
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Residues in contact with ASN2502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2498B ILE* 2.9 45.6 + - - +
2499B GLN* 3.5 7.3 - - - +
2501B ILE* 1.3 75.1 - - - +
2503B ARG* 1.3 57.1 + - - +
2505B ARG* 2.9 30.9 + - - +
2506B ASP* 2.8 39.4 + - - +
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Residues in contact with ARG2503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2332B TYR* 3.9 10.3 + - - -
2363B GLU* 2.7 40.5 + - + -
2499B GLN 2.9 15.6 + - - +
2500B ILE* 3.0 15.0 + - - +
2502B ASN* 1.3 76.0 - - - +
2504B VAL* 1.3 59.6 + - + +
2506B ASP* 3.6 12.5 + - - +
2507B LYS* 3.2 47.8 + - - +
2512B ASP* 2.8 40.0 + - - +
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Residues in contact with VAL2504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2333B ILE* 3.9 22.7 - - + +
2362B PHE* 4.3 24.5 - - + -
2415B MET* 3.5 21.8 - - + -
2418B LEU* 3.6 24.0 - - + -
2500B ILE 2.9 18.6 + - - +
2501B ILE* 3.6 9.6 - - + +
2502B ASN 3.2 0.2 - - - -
2503B ARG* 1.3 75.0 - - + +
2505B ARG* 1.3 58.9 + - - +
2507B LYS* 3.1 13.1 + - - +
2508B LEU* 3.0 36.3 + - + +
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Residues in contact with ARG2505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2411B LYS* 3.7 26.5 - - - +
2415B MET* 3.7 26.9 - - - -
2419B GLU* 4.1 7.3 + - - -
2501B ILE* 3.0 25.6 + - - +
2502B ASN* 2.9 35.5 + - - +
2504B VAL* 1.3 75.6 - - - +
2506B ASP* 1.3 52.0 + - - +
2508B LEU* 3.3 3.6 + - - +
2509B THR* 2.8 41.8 + - + +
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Residues in contact with ASP2506 (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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2502B ASN* 2.8 30.2 + - - +
2503B ARG* 3.6 17.5 + - - +
2504B VAL 3.2 0.2 - - - -
2505B ARG* 1.3 76.9 - - - +
2507B LYS* 1.3 56.4 + - - +
2509B THR* 3.4 4.8 + - - -
2510B GLY* 2.9 9.2 + - - -
2511B ARG* 2.8 62.0 + - - +
2512B ASP* 3.5 8.3 + - + -
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Residues in contact with LYS2507 (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* 2.7 63.9 + - + +
2333B ILE* 3.7 27.7 + - + +
2335B GLY* 3.9 4.2 - - - -
2362B PHE* 5.8 0.6 - - - +
2363B GLU* 3.4 23.9 + - - -
2404B MET* 4.6 5.2 - - - +
2408B ARG* 4.2 2.3 + - - -
2503B ARG* 3.2 41.1 + - - +
2504B VAL* 3.1 10.4 + - - +
2506B ASP* 1.3 76.6 - - - +
2508B LEU* 1.3 62.1 + - - +
2509B THR 3.3 1.5 + - - -
2510B GLY 3.7 1.9 + - - -
2512B ASP* 3.8 13.0 - - + -
2524B GLN* 2.9 23.9 + - - +
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Residues in contact with LEU2508 (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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2333B ILE* 3.8 34.8 - - + -
2404B MET* 5.7 1.1 - - - -
2407B LEU* 3.8 26.5 - - + +
2408B ARG* 3.0 28.0 - - + +
2411B LYS* 4.0 24.8 - - + +
2414B VAL* 4.2 13.5 - - + -
2415B MET* 3.6 30.3 - - + -
2504B VAL* 3.0 32.1 + - + +
2505B ARG* 3.3 6.0 + - - +
2507B LYS* 1.3 75.8 - - - +
2509B THR* 1.3 61.3 + - - +
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Residues in contact with THR2509 (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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2408B ARG* 3.5 15.4 + - - +
2411B LYS* 3.8 26.9 - - + +
2505B ARG* 2.8 26.5 + - + +
2506B ASP* 3.4 10.2 + - - -
2508B LEU* 1.3 81.9 - - - +
2510B GLY* 1.3 58.5 + - - +
2511B ARG* 3.9 15.6 + - - +
2518B THR* 3.5 21.4 - - - +
2519B LEU 4.1 0.2 - - - +
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Residues in contact with GLY2510 (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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2408B ARG* 3.2 19.8 - - - +
2506B ASP 2.9 3.4 + - - -
2507B LYS 3.7 2.8 + - - -
2509B THR* 1.3 78.8 - - - +
2511B ARG* 1.3 58.0 + - - +
2512B ASP* 3.4 18.1 + - - -
2517B ASP 3.7 1.7 - - - +
2518B THR* 3.6 2.9 - - - -
2519B LEU* 2.8 37.6 + - - +
2524B GLN* 4.3 3.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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