Contacts of the helix formed by residues 1233 - 1238 (chain B) in PDB entry 2VKZ
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 GLU1233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1227B GLY 4.4 0.3 - - - +
1228B ILE* 4.1 18.0 - - + +
1229B THR* 4.4 4.9 + - - +
1230B ASP* 2.8 18.0 + - + +
1231B PRO 2.8 0.6 + - - -
1232B TYR* 1.3 74.4 - - - +
1234B MET* 1.3 65.8 + - - +
1235B TYR 3.0 1.8 - - - -
1236B LYS* 3.0 26.5 + - + +
1237B TYR* 3.1 35.0 + - + -
1396B MET* 4.7 1.6 - - - -
1680B ARG* 2.4 38.1 + - - -
1731B LEU* 3.7 13.8 - - + +
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Residues in contact with MET1234 (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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1223B PHE* 3.7 37.0 - - + -
1228B ILE* 5.0 6.9 - - + +
1231B PRO* 2.8 18.8 + - - +
1233B GLU* 1.3 79.6 - - - +
1235B TYR* 1.3 62.9 + - + +
1237B TYR* 2.9 10.9 + - - +
1238B VAL* 2.8 29.1 + - - +
1243B VAL* 3.6 34.1 - - + -
1292B ILE* 4.9 6.7 - - + -
1326B ILE* 3.2 54.1 - - + -
1328B ILE* 5.9 1.8 - - + -
1388B MET* 5.9 0.4 - - + -
1396B MET* 4.6 8.4 - - + +
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Residues in contact with TYR1235 (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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1231B PRO 4.8 2.5 - - - -
1232B TYR* 3.0 35.0 + + + +
1233B GLU 3.0 1.4 - - - -
1234B MET* 1.3 80.2 - - + +
1236B LYS* 1.3 60.0 + - - +
1237B TYR 3.3 0.2 - - - -
1238B VAL 3.5 14.3 - - - +
1239B HIS 4.5 0.9 - - - -
1240B VAL* 3.9 30.7 - - + -
1243B VAL* 4.3 19.5 - - + -
1292B ILE* 2.7 34.0 + - + +
1293B SER 4.2 5.4 - - - -
1294B SER* 3.1 24.4 - - - -
1705B PRO* 3.9 23.1 - - + -
1721B ARG* 3.3 11.3 - - - +
1722B VAL* 2.9 37.7 + - + -
1733B PHE* 4.2 8.7 - + + -
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Residues in contact with LYS1236 (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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1232B TYR 3.7 0.6 + - - -
1233B GLU* 3.0 28.0 + - + +
1235B TYR* 1.3 81.7 - - - +
1237B TYR* 1.3 69.6 - - + +
1721B ARG* 3.2 17.6 - - - +
1722B VAL 3.6 21.8 - - - +
1723B SER* 5.3 0.7 - - - +
1724B LYS* 3.5 31.3 - - - +
1731B LEU* 3.8 37.8 - - + +
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Residues in contact with TYR1237 (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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1233B GLU* 3.1 49.8 + - + +
1234B MET 2.9 5.1 + - - +
1236B LYS* 1.3 89.7 - - + +
1238B VAL* 1.3 58.8 + - + +
1325B ARG* 3.1 18.4 + - - -
1392B LEU* 3.9 19.7 - - + -
1395B LYS* 4.1 26.5 + - + +
1396B MET* 3.5 61.7 + - + -
1680B ARG* 4.2 0.2 + - - -
1721B ARG* 3.2 12.9 + - - -
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Residues in contact with VAL1238 (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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1234B MET 2.8 14.2 + - - +
1235B TYR* 3.5 23.8 - - + +
1237B TYR* 1.3 85.9 - - + +
1239B HIS* 1.3 86.2 + - - +
1240B VAL 4.0 0.5 + - - -
1242B GLU* 3.4 34.1 - - + +
1243B VAL* 4.3 8.3 - - + -
1325B ARG* 3.8 15.5 - - + +
1326B ILE* 4.5 8.1 - - + -
1392B LEU* 3.6 31.2 - - + -
1720B ALA 4.4 0.9 - - - +
1721B ARG* 3.7 10.7 + - - +
1733B PHE* 5.7 0.2 - - - -
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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