Contacts of the helix formed by residues 1227 - 1237 (chain D) in PDB entry 5NPK
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 LYS1227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210D MET* 3.9 34.9 + - + +
1214D GLU* 3.1 43.4 + - - +
1226D GLY* 1.3 74.4 - - - +
1228D SER* 1.3 58.7 + - - +
1229D GLY 3.3 2.7 - - - -
1230D ILE* 3.4 12.3 + - + +
1231D ARG* 2.9 33.5 + - + +
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Residues in contact with SER1228 (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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1225D LEU 5.7 0.7 + - - -
1226D GLY* 3.6 2.8 - - - -
1227D LYS* 1.3 78.1 - - - +
1229D GLY* 1.3 64.0 + - - +
1231D ARG* 4.1 4.3 - - - +
1232D ARG* 3.3 32.0 + - - +
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Residues in contact with GLY1229 (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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1225D LEU 5.8 1.0 + - - -
1226D GLY 5.2 1.0 + - - -
1227D LYS 3.3 0.2 - - - -
1228D SER* 1.3 80.8 + - - +
1230D ILE* 1.3 65.1 + - - +
1232D ARG* 3.5 6.9 + - - +
1233D ALA* 3.0 24.9 + - - +
1239D GLY* 4.1 4.0 - - - -
1240D SER 3.2 26.7 - - - -
1241D ILE* 3.9 8.6 - - - +
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Residues in contact with ILE1230 (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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1210D MET* 4.0 6.7 - - + -
1214D GLU 3.9 21.3 - - - +
1215D GLY* 3.9 3.8 - - - -
1216D PRO* 4.0 12.6 - - + -
1224D ILE* 3.8 28.3 - - + -
1226D GLY 3.8 11.7 - - - +
1227D LYS* 3.4 14.5 + - + +
1229D GLY* 1.3 77.6 - - - +
1231D ARG* 1.3 57.9 + - - +
1233D ALA* 3.3 2.6 + - - +
1234D TYR* 2.9 59.5 + - + -
1241D ILE* 3.9 26.6 - - + +
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Residues in contact with ARG1231 (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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1207D ALA* 4.1 25.2 - - - +
1210D MET* 4.1 29.4 - - + -
1227D LYS* 2.9 19.5 + - - +
1228D SER* 4.1 5.4 - - - +
1230D ILE* 1.3 77.9 - - - +
1232D ARG* 1.3 58.5 + - + +
1234D TYR* 3.3 1.2 + - - +
1235D GLU* 2.9 45.9 + - + +
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Residues in contact with ARG1232 (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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1228D SER* 3.3 20.4 + - - +
1229D GLY* 3.9 6.1 - - - +
1231D ARG* 1.3 79.2 - - + +
1233D ALA* 1.3 58.2 + - - +
1235D GLU* 3.3 3.9 + - - -
1236D THR* 2.6 37.4 + - + +
1238D ARG* 3.3 20.6 + - - +
1239D GLY* 4.5 11.1 - - - -
1240D SER 5.3 2.1 - - - +
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Residues in contact with ALA1233 (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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1229D GLY 3.0 19.0 + - - +
1230D ILE* 3.6 6.3 - - - +
1232D ARG* 1.3 75.3 - - - +
1234D TYR* 1.3 64.9 + - + +
1237D GLY* 2.6 31.2 + - - -
1238D ARG 3.3 13.3 + - - -
1239D GLY* 4.0 4.5 - - - +
1241D ILE* 4.9 1.1 - - + -
1333D VAL* 3.6 38.6 - - + -
1335D MET* 3.8 4.9 - - - +
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Residues in contact with TYR1234 (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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1184D PRO* 5.7 2.9 - - + -
1186D HIS* 2.7 42.7 + + - -
1206D ILE* 3.3 21.7 - - + +
1210D MET* 3.7 17.9 - - + -
1213D ILE* 3.9 13.1 - - + +
1215D GLY* 3.1 22.5 + - - -
1216D PRO* 3.4 5.4 - - + +
1230D ILE* 2.9 39.4 + - + +
1231D ARG 3.9 2.5 - - - +
1232D ARG 3.3 0.2 - - - -
1233D ALA* 1.3 84.0 - - + +
1235D GLU* 1.3 58.4 + - - +
1241D ILE* 6.1 1.1 - - + -
1333D VAL* 6.3 0.9 - - + -
1335D MET* 4.7 11.2 - - + -
1347D ASN* 3.1 7.3 - - - +
1348D LEU* 3.0 61.1 + - + +
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Residues in contact with GLU1235 (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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1205D SER* 5.9 0.2 - - - -
1206D ILE* 3.5 36.8 + - + +
1207D ALA* 4.2 9.7 + - - +
1231D ARG* 2.9 36.2 + - + +
1232D ARG* 3.9 4.5 - - - +
1234D TYR* 1.3 79.4 - - - +
1236D THR* 1.3 66.3 + - + +
1347D ASN* 3.4 18.2 + - - +
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Residues in contact with THR1236 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1232D ARG* 2.6 23.5 + - + +
1235D GLU* 1.3 87.0 - - + +
1237D GLY* 1.3 59.1 + - - +
1238D ARG* 2.9 22.0 + - - +
1345D LEU* 3.8 20.6 - - - +
1346D ILE 4.7 1.4 - - - +
1347D ASN* 4.4 5.8 - - - -
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Residues in contact with GLY1237 (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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1233D ALA* 2.6 25.7 + - - -
1235D GLU 3.8 0.4 - - - -
1236D THR* 1.3 71.8 - - - +
1238D ARG* 1.3 60.2 + - - +
1333D VAL* 3.7 1.6 - - - +
1334D ASN* 3.4 6.4 + - - -
1335D MET* 2.9 32.5 + - - +
1345D LEU* 3.9 5.4 - - - -
1346D ILE 3.4 23.0 + - - -
1347D ASN* 4.1 1.4 - - - +
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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