Contacts of the helix formed by residues 1138 - 1147 (chain D) in PDB entry 7C17
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 LEU1138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789D LYS* 3.3 42.8 - - + +
792D ASN* 5.6 4.7 - - + -
793D SER* 3.7 18.2 - - - +
796D LEU* 4.0 24.0 - - + -
927D GLY* 4.3 7.0 - - - +
930D LEU* 3.7 37.3 - - + +
931D THR 4.7 3.5 + - - +
1137D GLY* 1.3 73.4 - - - +
1139D PRO* 1.3 69.3 - - + +
1141D VAL* 3.2 12.1 + - + -
1142D ALA* 2.9 26.6 + - + +
1241D TYR* 4.8 2.0 - - - +
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Residues in contact with PRO1139 (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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789D LYS* 3.5 36.3 - - + +
792D ASN* 5.6 7.6 - - - +
1137D GLY* 4.0 2.0 - - - -
1138D LEU* 1.3 89.5 - - + +
1140D ARG* 1.3 56.6 + - - +
1142D ALA* 3.4 7.3 + - + +
1143D ASP* 2.9 29.3 + - - +
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Residues in contact with ARG1140 (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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1137D GLY* 3.1 21.1 + - - +
1139D PRO* 1.3 75.8 - - - +
1141D VAL* 1.3 60.4 + - - +
1143D ASP* 3.8 7.0 - - + +
1144D LEU* 2.9 39.9 + - + +
1236D GLU* 3.9 22.2 - - - -
1240D VAL* 4.9 16.7 - - + +
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Residues in contact with VAL1141 (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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796D LEU* 4.2 9.2 - - + -
930D LEU* 5.0 4.0 - - + -
1137D GLY 2.8 20.5 + - - +
1138D LEU* 3.2 14.3 + - + +
1140D ARG* 1.3 77.3 - - - +
1142D ALA* 1.3 56.1 + - - +
1144D LEU* 3.3 5.8 + - - +
1145D PHE* 2.9 55.0 + - + -
1237D VAL* 4.0 16.2 - - + -
1240D VAL* 3.8 25.8 - - + -
1241D TYR* 3.8 23.3 - - + +
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Residues in contact with ALA1142 (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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792D ASN* 5.6 3.1 - - - +
796D LEU* 4.0 29.9 - - + +
799D ARG* 4.6 12.1 - - - +
1138D LEU* 2.9 16.1 + - + +
1139D PRO* 3.8 8.3 - - + +
1141D VAL* 1.3 75.8 - - - +
1143D ASP* 1.3 58.6 + - - +
1145D PHE* 3.8 1.3 - - - +
1146D GLU* 2.9 34.9 + - + +
1148D ARG* 4.6 3.1 - - - +
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Residues in contact with ASP1143 (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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1139D PRO 2.9 18.1 + - - +
1140D ARG* 3.9 7.4 - - - +
1142D ALA* 1.3 75.6 - - - +
1144D LEU* 1.3 55.0 + - - +
1147D ALA* 2.7 31.0 + - - -
1148D ARG* 3.5 38.3 + - - +
1149D ARG 3.6 23.2 + - - +
1150D PRO* 4.1 13.0 - - - +
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Residues in contact with LEU1144 (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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1140D ARG* 2.9 29.1 + - + +
1141D VAL* 3.8 3.8 - - - +
1143D ASP* 1.3 74.9 - - - +
1145D PHE* 1.3 69.4 + - + +
1147D ALA* 3.7 15.3 + - - +
1217D PRO* 5.3 5.6 - - + +
1232D TYR* 4.7 13.2 - - + +
1233D ILE* 3.8 43.5 - - + +
1236D GLU* 3.8 30.1 - - + -
1237D VAL* 3.8 25.6 - - + -
1240D VAL* 6.0 2.0 - - + -
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Residues in contact with PHE1145 (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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796D LEU* 4.4 10.1 - - + -
800D LEU* 3.7 38.6 - - + -
923D ILE* 3.6 36.6 - - + -
1141D VAL* 2.9 42.5 + - + +
1142D ALA* 3.8 5.6 - - - +
1143D ASP 3.3 0.2 - - - -
1144D LEU* 1.3 81.4 - - + +
1146D GLU* 1.3 64.8 + - + +
1147D ALA* 4.4 2.4 - - - +
1233D ILE* 5.3 1.3 - - + -
1237D VAL* 4.7 14.4 - - + -
1241D TYR* 4.6 0.9 - + - -
1253D ILE* 4.1 17.0 - - + -
1256D ILE* 4.5 12.3 - - + -
1257D VAL* 5.0 13.5 - - + -
1260D MET* 5.2 4.7 - - - +
1307D LEU 4.9 1.4 - - - +
1309D ILE* 3.3 21.2 - - + +
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Residues in contact with GLU1146 (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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796D LEU* 6.1 1.3 - - + -
799D ARG* 3.7 13.8 + - - +
1142D ALA* 2.9 18.6 + - + +
1143D ASP 4.0 0.4 - - - +
1145D PHE* 1.3 77.0 - - + +
1147D ALA* 1.3 68.9 + - - +
1148D ARG* 3.2 40.4 + - + +
1307D LEU 3.6 5.4 - - - +
1308D GLY* 3.3 28.6 + - - -
1309D ILE* 3.2 29.6 + - + +
1310D THR* 3.1 41.0 + - - +
1311D LYS* 5.4 1.4 - - - +
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Residues in contact with ALA1147 (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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1143D ASP 2.7 21.3 + - - -
1144D LEU* 3.8 11.7 - - - +
1145D PHE 3.4 2.8 - - - +
1146D GLU* 1.3 75.0 - - - +
1148D ARG* 1.3 58.3 + - - +
1149D ARG 3.8 0.4 - - - -
1217D PRO* 3.7 38.1 - - + +
1218D HIS* 2.8 27.0 + - - -
1233D ILE* 6.1 1.6 - - + -
1306D LEU* 4.8 15.7 - - + +
1307D LEU 5.3 0.7 - - - +
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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