Contacts of the helix formed by residues 2410 - 2423 (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 HIS2410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2208B LEU* 3.6 46.0 + - + +
2211B ASN* 5.9 4.6 - - + +
2212B ASP* 6.0 1.8 - - - +
2406B VAL* 3.1 28.9 + - + +
2407B LEU 3.2 4.5 - - - -
2409B GLU* 1.3 108.8 + - + +
2411B LYS* 1.3 63.1 - - - +
2412B ASP* 3.3 3.3 + - - +
2413B SER* 3.6 12.0 + - - +
2414B VAL* 3.4 23.0 + - - +
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Residues in contact with LYS2411 (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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2407B LEU 3.0 10.2 + - - +
2408B ARG* 3.3 18.4 - - - +
2409B GLU 3.4 3.5 + - - +
2410B HIS* 1.3 76.4 - - - +
2412B ASP* 1.3 76.9 + - - +
2414B VAL* 3.3 3.1 + - - +
2415B MET* 2.8 43.7 + - - +
2505B ARG* 3.7 30.5 - - - +
2508B LEU* 4.0 31.6 - - + +
2509B THR* 3.8 20.2 - - + +
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Residues in contact with ASP2412 (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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1791B HIS* 5.4 3.7 + - - +
1795B VAL* 5.2 9.0 - - - +
1799B GLU* 5.6 1.2 - - - +
1901B GLN* 3.6 25.3 + - - +
1905B ARG* 3.9 8.0 + - - +
2409B GLU 5.3 0.2 + - - -
2410B HIS* 3.3 0.8 - - - +
2411B LYS* 1.3 99.0 - - - +
2413B SER* 1.3 56.9 + - - +
2415B MET* 3.5 6.7 + - - +
2416B ALA* 2.9 28.9 + - - +
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Residues in contact with SER2413 (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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1901B GLN* 3.2 31.3 + - - +
2204B LEU* 3.5 23.5 - - - +
2208B LEU* 5.2 2.6 - - - +
2410B HIS* 3.6 20.9 + - - +
2411B LYS 3.4 0.6 - - - -
2412B ASP* 1.3 74.2 - - - +
2414B VAL* 1.3 65.8 + - - +
2416B ALA* 3.4 3.1 + - - +
2417B VAL* 3.2 28.2 + - - +
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Residues in contact with VAL2414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B LEU* 4.4 11.9 - - + -
2204B LEU* 4.3 9.2 - - + -
2205B VAL* 4.8 5.4 - - + -
2208B LEU* 4.3 14.8 - - + -
2333B ILE* 4.3 9.9 - - + -
2407B LEU* 4.0 26.9 - - + +
2410B HIS 3.4 14.6 + - - +
2411B LYS* 3.3 8.6 + - - +
2413B SER* 1.3 75.1 - - - +
2415B MET* 1.3 63.8 + - - +
2417B VAL* 3.4 4.2 + - - +
2418B LEU* 3.1 42.2 + - + +
2508B LEU* 4.2 15.9 - - + -
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Residues in contact with MET2415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905B ARG* 4.5 4.0 - - - +
2411B LYS* 2.8 33.6 + - - +
2412B ASP* 3.6 7.4 - - - +
2414B VAL* 1.3 73.9 - - - +
2416B ALA* 1.3 59.7 + - - +
2418B LEU* 4.0 5.2 - - + +
2419B GLU* 2.8 45.8 + - + +
2501B ILE* 3.7 30.5 - - + +
2504B VAL* 3.5 25.1 - - + -
2505B ARG* 3.7 45.5 - - - -
2508B LEU* 3.6 11.9 - - + -
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Residues in contact with ALA2416 (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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1901B GLN* 3.6 27.8 - - + -
1904B LEU* 3.8 15.8 - - + +
1905B ARG* 3.8 22.0 - - - +
2412B ASP 2.9 17.7 + - - +
2413B SER 3.5 5.8 - - - +
2414B VAL 3.3 0.2 - - - -
2415B MET* 1.3 75.9 - - - +
2417B VAL* 1.3 57.9 + - - +
2419B GLU* 3.9 3.4 - - - +
2420B ALA* 3.1 27.9 + - - +
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Residues in contact with VAL2417 (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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1900B LEU* 3.8 14.1 - - + -
1904B LEU* 3.7 22.7 - - + -
2197B ARG 4.8 0.4 - - - +
2200B GLN* 4.8 8.1 - - + +
2201B LEU* 3.9 31.0 - - + +
2204B LEU* 3.5 21.1 - - + -
2413B SER 3.2 13.7 + - - +
2414B VAL 3.7 6.5 - - - +
2416B ALA* 1.3 75.1 - - - +
2418B LEU* 1.3 64.8 + - - +
2420B ALA* 3.2 11.8 + - - +
2421B PHE* 3.2 37.9 - - + -
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Residues in contact with LEU2418 (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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2201B LEU* 4.0 12.3 - - + -
2333B ILE* 4.2 10.1 - - + +
2334B LEU* 3.8 21.1 - - + -
2362B PHE* 3.9 15.7 - - + -
2414B VAL* 3.1 34.8 + - + +
2415B MET* 4.0 5.8 - - + +
2417B VAL* 1.3 72.9 - - - +
2419B GLU* 1.3 59.8 + - - +
2421B PHE* 3.1 34.8 + - + -
2422B VAL* 2.9 33.9 + - + +
2501B ILE* 5.4 1.8 - - + -
2504B VAL* 3.6 34.3 - - + -
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Residues in contact with GLU2419 (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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1905B ARG* 2.8 35.8 + - - +
2415B MET* 2.8 32.9 + - + +
2416B ALA 3.9 3.4 - - - +
2418B LEU* 1.3 73.0 - - - +
2420B ALA* 1.3 61.8 + - - +
2422B VAL 4.5 0.4 - - - +
2423B TYR* 3.2 40.7 + - + +
2501B ILE* 3.7 46.5 - - + +
2505B ARG* 4.1 10.7 + - - -
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Residues in contact with ALA2420 (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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1904B LEU* 3.8 27.1 - - + -
1941B GLN* 4.2 17.4 - - + +
1945B ARG* 5.7 0.7 + - - -
2416B ALA 3.1 16.6 + - - +
2417B VAL* 3.3 12.3 - - - +
2418B LEU 3.1 0.2 - - - -
2419B GLU* 1.3 77.7 - - - +
2421B PHE* 1.3 57.0 + - + +
2423B TYR* 4.2 1.8 - - - +
2424B ASP* 3.7 21.5 + - - +
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Residues in contact with PHE2421 (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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1941B GLN* 5.1 4.7 - - - +
2197B ARG* 3.4 55.2 - - + +
2198B VAL* 4.8 5.4 - - + -
2200B GLN* 5.8 0.9 - - - -
2201B LEU* 4.6 5.2 - - + -
2334B LEU* 4.5 10.5 - - + -
2362B PHE* 3.8 15.7 - + - -
2417B VAL* 3.2 35.6 + - + -
2418B LEU* 3.1 38.6 + - + -
2420B ALA* 1.3 77.2 - - - +
2422B VAL* 1.3 64.9 + - - +
2423B TYR 3.6 0.2 - - - -
2424B ASP* 3.7 15.5 - - + +
2427B LEU* 4.1 7.4 - - + +
2430B ARG* 3.0 43.0 + - - +
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Residues in contact with VAL2422 (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* 3.4 35.0 - - + -
2418B LEU* 2.9 18.8 + - + +
2419B GLU 3.5 0.9 + - - +
2421B PHE* 1.3 78.7 - - - +
2423B TYR* 1.3 56.9 + - - +
2424B ASP 3.1 4.0 + - - +
2427B LEU 5.2 0.2 - - - +
2428B ASN* 2.9 25.6 - - - +
2430B ARG* 5.2 1.3 - - - +
2431B LEU* 4.5 14.2 - - + +
2497B ALA* 3.7 28.2 - - + +
2500B ILE* 4.3 7.4 - - + -
2501B ILE* 3.6 36.1 - - + -
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Residues in contact with TYR2423 (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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1945B ARG* 3.0 25.9 + - - +
2419B GLU* 3.2 35.5 + - + +
2420B ALA* 4.2 3.6 - - - +
2422B VAL* 1.3 73.3 - - - +
2424B ASP* 1.3 60.2 + - - +
2425B PRO* 3.6 1.2 - - - +
2428B ASN* 4.4 5.9 + - - +
2494B ASN* 4.3 15.7 - - - -
2497B ALA* 3.5 27.1 - - + -
2498B ILE* 3.6 22.1 - - - +
2501B ILE* 3.2 29.0 - - + +
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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
------------------------------------------------------------
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