Contacts of the helix formed by residues 2212 - 2218 (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 ASP2212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2208B LEU 3.0 13.3 + - - +
2209B LEU 3.2 4.0 - - - +
2210B ALA 3.5 0.4 - - - -
2211B ASN* 1.3 74.7 - - - +
2213B PRO* 1.4 68.7 - - - +
2214B THR* 4.0 11.7 + - - -
2215B SER* 3.0 29.3 + - - +
2216B LEU* 2.9 25.5 + - - +
2402B THR* 4.0 3.6 - - - +
2406B VAL* 3.3 29.8 - - + +
2409B GLU* 5.0 8.7 - - - +
2410B HIS* 6.0 1.8 + - - +
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Residues in contact with PRO2213 (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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1627B GLN* 4.2 28.9 - - - +
2211B ASN 3.4 9.2 - - - +
2212B ASP* 1.4 91.4 - - - +
2214B THR* 1.3 54.5 + - - +
2216B LEU* 3.1 8.8 + - + +
2217B ARG* 2.7 36.9 + - - +
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Residues in contact with THR2214 (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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2212B ASP* 3.5 11.7 + - - -
2213B PRO* 1.3 78.6 - - - +
2215B SER* 1.3 60.6 + - - +
2217B ARG* 3.4 11.0 - - + +
2218B LYS* 3.3 45.5 + - + +
2402B THR* 4.0 13.9 - - + +
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Residues in contact with SER2215 (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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2209B LEU* 3.1 50.9 - - - +
2212B ASP* 3.0 19.9 + - - -
2213B PRO 3.2 0.4 - - - -
2214B THR* 1.3 76.4 - - - +
2216B LEU* 1.3 60.0 + - - +
2218B LYS 3.4 0.9 + - - -
2219B ASN 3.3 3.5 + - - -
2220B LEU* 3.0 42.9 + - - +
2402B THR* 3.6 13.2 - - - +
2406B VAL* 3.7 2.3 - - - +
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Residues in contact with LEU2216 (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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2209B LEU 3.5 2.2 + - - -
2210B ALA* 3.5 39.9 - - + +
2211B ASN 6.0 0.2 - - - -
2212B ASP 2.9 8.5 + - - +
2213B PRO* 3.6 11.4 - - + +
2215B SER* 1.3 73.4 - - - +
2217B ARG* 1.3 66.1 + - - +
2218B LYS 3.2 0.2 - - - -
2219B ASN* 3.2 20.2 + - - +
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Residues in contact with ARG2217 (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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1426B PRO* 5.5 8.7 - - - +
1583B TYR* 4.7 11.9 + - - -
2213B PRO 2.7 20.9 + - - +
2214B THR* 3.4 14.6 - - + +
2216B LEU* 1.3 73.6 - - - +
2218B LYS* 1.3 67.7 + - + +
2219B ASN* 3.7 5.0 + - - -
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Residues in contact with LYS2218 (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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1427B GLU* 3.4 31.9 + - - +
2214B THR* 3.3 35.2 + - - +
2215B SER 3.4 0.4 + - - -
2216B LEU 3.2 1.0 - - - -
2217B ARG* 1.3 85.3 - - + +
2219B ASN* 1.3 70.6 + - - +
2220B LEU* 3.2 21.8 + - + +
2322B ARG* 3.6 41.2 + - - +
2398B ILE* 3.7 26.5 + - - +
2399B THR* 4.4 4.7 + - - +
2402B THR* 3.3 25.8 + - - -
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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