Contacts of the helix formed by residues 1219 - 1225 (chain D) in PDB entry 5UH6
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 SER1219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1217D THR* 3.2 14.2 + - - +
1218D ASP* 1.3 81.4 + - - +
1220D TRP* 1.3 57.0 + - - +
1221D LEU 3.2 0.7 + - - -
1222D SER* 2.7 23.0 + - - -
1223D ALA* 3.0 19.8 + - - +
1243D ASP* 3.0 33.5 + - - -
1250D GLU* 3.1 29.3 - - - +
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Residues in contact with TRP1220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125C LEU* 6.0 0.2 - - + -
1128C LEU* 4.3 19.1 - - + -
1135C VAL* 4.5 3.8 - - + -
10D LEU* 3.5 35.2 + - + -
12D ILE* 3.4 48.9 - - + +
413D PHE* 5.5 1.6 - + - -
1218D ASP 3.9 3.1 + - - -
1219D SER* 1.3 72.2 - - - +
1221D LEU* 1.3 73.4 - - + +
1223D ALA* 3.7 8.2 - - - +
1224D ALA* 2.7 38.9 + - + +
1232D VAL* 3.7 6.6 - - + +
1233D LEU* 4.0 23.8 - - + -
1236D ALA* 4.1 18.4 - - + -
1241D ARG* 3.9 31.0 + - + +
1242D SER 4.7 0.4 - - - -
1243D ASP* 3.2 31.1 - - + +
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Residues in contact with LEU1221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121C PHE* 4.8 1.6 - - + -
1124C LEU* 4.9 9.2 - - + -
1125C LEU* 6.4 0.2 - - + -
10D LEU* 4.3 19.1 - - + -
413D PHE* 4.5 17.1 - - + -
1219D SER* 3.1 8.0 - - - +
1220D TRP* 1.3 111.2 - - + +
1222D SER* 1.3 52.5 + - - +
1224D ALA* 4.2 1.6 - - - +
1225D SER* 2.4 36.7 + - - -
1243D ASP* 3.5 13.9 - - - +
1245D LEU* 4.3 10.1 - - + -
1250D GLU* 4.4 15.9 - - + +
1253D ILE* 3.8 30.7 - - + +
1254D ILE* 4.6 5.6 - - + -
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Residues in contact with SER1222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879D ASP* 3.9 13.0 + - - +
882D GLN* 4.5 2.8 + - - -
883D ASP* 5.4 3.0 + - - -
1217D THR* 4.3 12.6 + - - +
1219D SER* 2.7 29.7 + - - -
1221D LEU* 1.3 73.9 - - - +
1223D ALA* 1.3 59.3 + - - +
1225D SER* 3.5 10.3 + - - -
1226D PHE* 3.7 11.3 - - - +
1249D LYS* 3.5 28.3 - - - +
1250D GLU* 3.9 17.6 + - - +
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Residues in contact with ALA1223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214D SER 4.6 3.6 - - - +
1215D LEU* 3.9 18.6 - - - +
1217D THR* 3.8 15.0 - - + +
1219D SER 3.0 14.9 + - - +
1220D TRP* 3.7 6.5 - - - +
1221D LEU 3.1 0.2 - - - -
1222D SER* 1.3 77.3 - - - +
1224D ALA* 1.3 63.7 + - - +
1225D SER 3.2 1.6 - - - -
1226D PHE* 3.1 20.0 + - - +
1227D GLN 3.6 12.1 + - - +
1232D VAL* 3.8 19.2 - - + +
1241D ARG* 5.5 1.8 - - - +
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Residues in contact with ALA1224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D PHE* 4.1 20.1 - - + +
414D ARG* 5.6 0.9 - - - +
1220D TRP* 2.7 23.4 + - + +
1221D LEU* 4.3 2.9 - - - +
1223D ALA* 1.3 73.5 - - - +
1225D SER* 1.3 57.6 + - - +
1226D PHE 3.1 5.2 + - - -
1229D THR* 3.0 47.0 + - + +
1232D VAL* 3.6 19.4 - - + +
1233D LEU* 4.2 9.9 - - + -
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Residues in contact with SER1225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D PHE* 4.1 24.9 - - - -
414D ARG* 3.7 10.9 - - - +
418D LEU* 3.4 40.5 - - - +
875D ARG* 4.0 2.8 + - - -
1221D LEU 2.4 27.8 + - - -
1222D SER 3.5 0.9 + - - -
1224D ALA* 1.3 76.2 - - - +
1226D PHE* 1.3 57.8 + - - +
1249D LYS* 3.3 24.1 - - - +
1253D ILE* 4.1 4.7 - - - +
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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