Contacts of the helix formed by residues 1201 - 1206 (chain D) in PDB entry 4OIO
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 CYS1201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107D VAL* 3.9 3.3 - - - +
1109D GLU* 3.3 16.8 - - + +
1110D ALA 3.9 6.1 - - - +
1112D CYS 3.7 18.4 - - - +
1189D ARG* 3.8 5.6 - - - -
1194D CYS* 3.3 4.8 - - - -
1196D THR* 3.2 14.8 - - - +
1200D VAL* 1.3 82.5 - - - +
1202D GLN* 1.3 63.3 + - - +
1203D LYS 3.6 3.8 - - - -
1204D CYS* 3.3 20.6 - - - -
1205D TYR* 3.4 22.5 + - - +
2001D ZN 2.4 31.2 - - - -
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Residues in contact with GLN1202 (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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1107D VAL* 4.1 10.5 - - + -
1109D GLU 3.0 7.2 + - - +
1110D ALA* 3.3 24.0 + - - +
1165D TYR* 3.6 13.1 + - - +
1201D CYS* 1.3 76.1 - - - +
1203D LYS* 1.3 87.9 + - - +
1205D TYR* 3.6 1.2 + - - +
1206D GLY* 3.1 23.6 + - - -
1214D PRO* 4.8 6.6 - - - +
1215D VAL* 2.9 35.5 - - + +
1216D SER* 4.8 0.7 - - - -
1217D ILE* 4.1 15.2 + - + +
14E ASP 4.8 6.1 - - - +
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Residues in contact with LYS1203 (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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1110D ALA* 3.4 17.9 + - - +
1111D ASP* 3.8 18.8 - - - +
1148D VAL* 3.3 35.0 + - + +
1163D GLY* 5.5 2.2 + - - +
1165D TYR* 2.8 38.3 + - + +
1189D ARG* 3.4 32.1 - - - +
1201D CYS* 3.4 0.8 - - - -
1202D GLN* 1.3 97.5 - - - +
1204D CYS* 1.3 65.5 + - - +
1205D TYR 3.4 0.2 + - - -
1206D GLY 3.8 2.4 + - - -
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Residues in contact with CYS1204 (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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1112D CYS* 3.9 1.6 - - - -
1114D THR* 4.0 4.0 - - - -
1147D ARG* 5.3 0.2 + - - -
1189D ARG* 2.9 48.1 - - - +
1190D SER 3.8 9.2 - - - +
1191D PRO* 3.4 14.4 - - - +
1193D THR* 5.7 0.2 - - - -
1194D CYS* 3.3 28.5 - - + -
1200D VAL* 3.9 4.9 - - + -
1201D CYS* 3.3 5.3 - - - -
1203D LYS* 1.3 78.9 - - - +
1205D TYR* 1.3 61.6 + - - +
2001D ZN 2.2 37.5 - - - -
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Residues in contact with TYR1205 (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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772D PRO 5.3 0.5 + - - -
1107D VAL* 5.1 0.4 - - + -
1146D GLY 4.0 2.3 - - - +
1147D ARG* 4.6 9.1 + - - +
1189D ARG 5.3 0.4 - - - -
1191D PRO* 4.7 6.9 - - + +
1200D VAL* 4.3 11.2 - - + +
1201D CYS 3.4 16.5 + - - +
1202D GLN 3.9 2.9 - - - +
1203D LYS 3.2 0.4 - - - -
1204D CYS* 1.3 83.4 - - - +
1206D GLY* 1.3 69.9 + - - +
1207D TYR 3.3 17.0 - - - -
1208D ASP* 4.5 3.8 - - - -
1209D LEU* 5.5 2.0 + - - +
1215D VAL* 3.7 22.9 - - + -
1219D GLU* 5.2 4.9 + - - -
1221D VAL* 3.4 45.8 + - + +
1224D VAL* 4.7 8.0 - - - +
1366D LYS* 3.1 43.7 + - + +
1367D HIS* 3.7 23.8 + - - -
1370D ILE* 4.5 10.5 - - + -
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Residues in contact with GLY1206 (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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1146D GLY 3.2 8.7 - - - -
1147D ARG* 4.4 4.3 - - - -
1148D VAL* 4.6 0.4 - - - -
1165D TYR* 3.8 23.6 - - - -
1202D GLN 3.1 8.1 + - - +
1203D LYS 3.8 4.8 + - - -
1204D CYS 3.7 1.0 - - - -
1205D TYR* 1.3 77.3 - - - +
1207D TYR* 1.3 70.0 + - - +
1214D PRO* 4.0 0.2 - - - +
1215D VAL* 3.2 24.1 + - - +
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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