Contacts of the helix formed by residues 1216 - 1225 (chain D) in PDB entry 7KHC
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 ALA1216 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1149D ARG* 3.6 42.2 - - + +
1150D PRO* 4.5 7.5 - - + +
1153D PRO* 4.7 11.6 - - + +
1214D PRO 4.0 1.6 + - - -
1215D GLU* 1.3 72.0 - - - +
1217D PRO* 1.3 66.7 - - + +
1218D HIS* 2.8 6.8 + - + +
1219D ASP* 2.2 38.4 + - - +
1220D ILE* 3.9 0.4 - - - +
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Residues in contact with PRO1217 (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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1144D LEU* 5.5 4.5 - - + +
1147D ALA* 4.5 27.1 - - + -
1148D ARG 5.3 4.7 - - - +
1150D PRO* 5.9 0.2 - - + -
1215D GLU 3.6 6.0 - - - +
1216D ALA* 1.3 82.2 - - + +
1218D HIS* 1.3 65.3 + - + +
1220D ILE* 3.0 13.5 + - + +
1221D LEU* 2.9 25.2 + - - +
1229D VAL* 4.3 10.4 - - + +
1232D TYR* 4.5 11.4 - - + +
1233D ILE* 4.5 17.7 - - + -
1306D LEU* 4.1 24.7 - - + -
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Residues in contact with HIS1218 (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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1147D ALA* 4.0 17.9 + - - +
1149D ARG* 3.4 52.4 + - + +
1216D ALA* 2.8 5.6 + - + +
1217D PRO* 1.3 79.7 - - + +
1219D ASP* 1.3 63.0 + - - +
1221D LEU* 3.3 4.8 + - - +
1222D ARG* 3.0 26.8 + - - +
1306D LEU* 3.4 44.5 + - + +
1307D LEU* 5.7 0.2 - - - -
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Residues in contact with ASP1219 (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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1154D ALA 4.1 7.6 - - - +
1156D LEU* 3.5 31.1 + - + +
1215D GLU* 4.1 6.4 - - - +
1216D ALA* 2.2 34.6 + - + +
1218D HIS* 1.3 77.5 - - - +
1220D ILE* 1.3 89.0 + - - +
1222D ARG* 4.4 12.1 - - - +
1223D LEU* 2.8 44.0 + - + +
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Residues in contact with ILE1220 (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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1156D LEU* 5.1 7.0 - - + -
1215D GLU* 3.8 30.3 - - + -
1216D ALA 3.9 3.8 - - - +
1217D PRO* 3.0 14.0 + - + +
1219D ASP* 1.3 98.3 + - - +
1221D LEU* 1.3 62.5 + - - +
1224D ARG* 2.9 52.9 + - + +
1225D GLY 3.2 5.4 + - - -
1228D ALA* 4.1 10.8 - - + +
1229D VAL* 3.5 34.3 - - + +
1232D TYR* 5.1 11.7 - - + -
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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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1217D PRO 2.9 14.9 + - - +
1218D HIS* 3.8 4.3 - - - +
1220D ILE* 1.3 76.5 - - - +
1222D ARG* 1.3 66.2 + - - +
1225D GLY* 3.1 24.5 + - - -
1226D VAL* 3.6 41.5 - - + +
1229D VAL* 3.7 16.3 - - + +
1261D LEU* 3.8 26.5 - - + -
1304D ARG* 4.1 22.7 - - + +
1305D ASP* 4.0 13.9 - - - -
1306D LEU* 4.0 15.7 - - + +
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Residues in contact with ARG1222 (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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1158D GLU* 5.3 9.3 - - - +
1206D ARG* 4.8 5.1 + - - +
1218D HIS* 3.0 18.9 + - - +
1219D ASP* 4.4 13.7 - - - +
1221D LEU* 1.3 80.7 - - - +
1223D LEU* 1.3 90.9 + - + +
1225D GLY* 4.6 0.9 + - - -
1303D SER* 6.4 1.8 - - - -
1304D ARG 5.7 4.5 - - - +
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Residues in contact with LEU1223 (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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1156D LEU* 5.4 6.7 - - + -
1157D ALA 3.6 12.1 - - - +
1158D GLU* 3.6 33.2 - - + +
1206D ARG* 3.5 39.7 + - - +
1207D GLY* 5.0 7.2 - - - -
1219D ASP* 2.8 30.5 + - + +
1220D ILE* 5.3 0.2 - - - -
1222D ARG* 1.3 115.6 - - + +
1224D ARG* 1.3 68.8 + - + +
1225D GLY* 4.7 0.2 - - - -
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Residues in contact with ARG1224 (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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1156D LEU* 4.0 15.9 - - + +
1206D ARG 5.9 0.4 - - - +
1207D GLY* 3.9 28.9 + - - -
1209D VAL* 5.8 0.6 - - - +
1220D ILE* 2.9 38.8 + - + +
1223D LEU* 1.3 81.3 - - + +
1225D GLY* 1.3 59.7 + - - +
1228D ALA* 3.6 26.9 - - + +
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Residues in contact with GLY1225 (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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1220D ILE 3.2 4.3 + - - +
1221D LEU* 3.1 22.5 + - - -
1222D ARG 5.1 0.7 - - - -
1223D LEU 3.4 1.3 - - - -
1224D ARG* 1.3 79.0 - - - +
1226D VAL* 1.3 69.5 + - - +
1227D HIS 3.5 1.3 - - - -
1228D ALA* 3.4 4.2 + - - +
1229D VAL* 3.3 18.7 + - - +
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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