Contacts of the helix formed by residues 2380 - 2387 (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 THR2380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2378B ARG* 3.3 32.0 - - - +
2379B LEU* 1.3 77.2 - - - +
2381B ARG* 1.3 54.7 + - - +
2383B LEU* 3.3 23.6 + - + +
2384B THR* 2.8 31.6 + - - -
2538B LEU* 5.1 8.7 - - - -
2545B TRP* 5.1 6.5 - - - -
2546B CYS 4.1 0.3 + - - -
2547B PRO 3.1 24.8 + - - -
2549B TRP 2.8 35.4 + - - +
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Residues in contact with ARG2381 (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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2264B GLU* 3.4 15.4 + - - +
2291B VAL* 3.1 49.5 + - + +
2294B THR* 2.7 34.5 + - - -
2295B ALA 3.9 6.9 + - - -
2296B GLY* 3.5 25.6 - - - +
2380B THR* 1.3 78.4 + - - +
2382B MET* 1.3 63.0 + - + +
2384B THR* 3.2 8.9 + - - -
2385B ASN* 2.8 30.3 + - - +
2538B LEU* 6.1 0.8 - - - +
2547B PRO 5.0 2.0 + - - +
2548B PHE* 2.8 28.5 + - - +
2549B TRP 3.4 7.9 - - - +
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Residues in contact with MET2382 (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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2246B LEU* 6.0 1.3 - - + -
2250B ILE* 3.6 28.3 - - + -
2254B ARG* 3.6 28.0 - - - +
2264B GLU* 4.5 2.2 - - - +
2295B ALA 3.9 12.3 - - - +
2296B GLY* 3.9 21.3 - - - +
2297B ASP* 5.6 0.4 - - - +
2298B ASP* 3.7 22.9 - - - +
2299B LEU* 3.7 19.0 - - + +
2300B ALA 4.6 0.9 + - - -
2381B ARG* 1.3 72.2 - - + +
2383B LEU* 1.3 62.2 + - + +
2385B ASN* 4.0 1.3 - - - +
2386B ALA* 3.1 27.9 + - - +
2548B PHE 4.2 12.1 - - - +
2549B TRP* 2.8 37.7 + - + +
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Residues in contact with LEU2383 (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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2246B LEU* 3.9 21.1 - - + -
2299B LEU* 3.7 16.6 - - + -
2320B TYR* 2.9 34.5 + - + +
2324B LEU* 4.0 22.0 - - + -
2344B LEU* 4.8 8.5 - - + -
2346B LEU* 5.8 0.2 - - + -
2353B ILE* 5.3 0.2 - - + -
2378B ARG* 3.5 47.1 - - + +
2379B LEU* 5.0 2.5 - - + -
2380B THR* 3.3 20.9 + - + +
2382B MET* 1.3 75.4 - - + +
2384B THR* 1.3 64.9 + - - +
2386B ALA 3.5 0.5 + - - -
2387B MET* 3.5 19.9 + - - +
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Residues in contact with THR2384 (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* 3.7 16.6 + - - +
2380B THR 2.8 22.3 + - - -
2381B ARG* 3.4 10.5 - - - -
2383B LEU* 1.3 73.8 - - - +
2385B ASN* 1.3 65.7 + - - +
2387B MET* 3.2 29.9 + - + +
2388B GLU 4.6 2.8 - - - +
2391B GLY* 5.6 0.2 - - - -
2392B LEU* 3.5 36.9 - - + +
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Residues in contact with ASN2385 (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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1405B GLN* 3.5 26.1 + - - +
2296B GLY 3.5 21.6 - - - +
2297B ASP* 3.7 15.8 - - - +
2300B ALA* 3.2 22.5 - - + +
2381B ARG 2.8 20.0 + - - +
2382B MET* 4.0 3.8 - - - +
2384B THR* 1.3 73.8 - - - +
2386B ALA* 1.3 57.0 + - - +
2387B MET 2.9 14.6 - - - +
2389B VAL* 5.5 3.8 + - - +
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Residues in contact with ALA2386 (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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2299B LEU* 3.7 26.9 - - + -
2300B ALA* 3.8 18.8 - - - +
2303B LEU* 4.4 8.8 - - + +
2317B ARG* 3.2 23.6 - - - +
2320B TYR* 3.8 13.3 - - + -
2382B MET 3.1 18.9 + - - +
2383B LEU 3.7 4.9 - - - +
2384B THR 3.2 0.6 - - - -
2385B ASN* 1.3 72.7 - - - +
2387B MET* 1.3 65.4 + - - +
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Residues in contact with MET2387 (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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2317B ARG* 4.0 8.6 + - - +
2320B TYR* 4.0 8.1 - - + -
2321B THR* 3.3 28.7 - - + +
2324B LEU* 4.4 9.4 - - - -
2379B LEU* 4.7 3.8 - - - -
2383B LEU 3.5 17.0 + - - +
2384B THR* 3.2 17.7 + - + +
2385B ASN 2.9 15.5 - - - +
2386B ALA* 1.3 79.6 - - - +
2388B GLU* 1.3 69.3 + - - +
2389B VAL* 3.7 1.2 + - - +
2391B GLY* 3.4 8.5 - - - -
2392B LEU* 3.3 45.8 - - + +
2396B TYR* 3.6 30.1 - - + -
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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