Contacts of the helix formed by residues 1191 - 1202 (chain C) in PDB entry 5NSS
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 LYS1191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673C HIS* 5.4 3.6 - - + +
1189C GLY 4.4 7.7 + - - +
1190C ALA* 1.3 78.3 - - - +
1192C GLU* 1.3 74.3 + - - +
1193C ALA* 3.0 10.4 + - + +
1194C GLU* 3.0 27.8 + - + +
1195C ILE* 2.9 23.3 + - - +
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Residues in contact with GLU1192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673C HIS* 3.8 11.9 + - - -
1113C LEU* 3.7 18.1 - - + +
1191C LYS* 1.3 78.1 - - - +
1193C ALA* 1.3 56.1 + - - +
1195C ILE* 3.7 9.4 - - - -
1196C LYS* 2.9 38.0 + - + +
641D ILE* 3.7 31.9 - - + -
764D ARG* 3.3 67.3 + - - +
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Residues in contact with ALA1193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191C LYS* 3.0 9.9 - - + +
1192C GLU* 1.3 78.8 - - - +
1194C GLU* 1.3 61.1 + - + +
1196C LYS* 3.8 2.3 - - - +
1197C GLU* 2.9 29.3 + - - +
764D ARG* 5.6 0.2 - - - +
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Residues in contact with GLU1194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 5.0 15.8 - - + +
1151C LEU* 5.6 1.6 - - + +
1152C GLY* 5.0 9.9 - - - -
1153C ALA* 4.1 26.3 + - - +
1155C VAL* 5.6 7.0 - - - +
1190C ALA* 5.0 9.2 - - + +
1191C LYS* 3.0 31.1 + - + +
1193C ALA* 1.3 77.2 - - + +
1195C ILE* 1.3 61.1 + - + +
1197C GLU* 3.8 11.2 - - + +
1198C LEU* 2.9 30.7 + - - +
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Residues in contact with ILE1195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 6.0 0.2 - - + -
670C PHE* 4.1 8.7 - - + -
1113C LEU* 3.7 32.5 - - + -
1116C HIS* 4.9 8.3 - - + -
1117C LEU* 3.7 52.5 - - + +
1120C ALA* 4.8 1.4 - - + +
1190C ALA* 3.8 16.6 - - + +
1191C LYS 2.9 26.3 + - - +
1192C GLU* 3.9 5.4 - - - +
1193C ALA 3.2 0.2 - - - -
1194C GLU* 1.3 77.8 - - - +
1196C LYS* 1.3 62.0 + - + +
1198C LEU* 3.9 4.5 - - - +
1199C LEU* 2.9 33.9 + - + +
641D ILE* 5.3 2.9 - - + -
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Residues in contact with LYS1196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C HIS* 5.9 2.2 - - - -
1192C GLU* 2.9 23.4 + - - +
1193C ALA* 4.2 2.7 - - - +
1195C ILE* 1.3 74.9 - - + +
1197C GLU* 1.3 59.4 + - - +
1199C LEU* 4.4 5.8 - - + -
1200C LYS* 2.9 30.5 + - - +
1206C THR* 3.6 42.2 + - + +
1207C SER* 4.2 15.2 + - - +
641D ILE* 3.7 50.0 - - + +
642D ASP* 5.1 5.5 - - - +
764D ARG* 5.8 0.7 - - - +
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Residues in contact with GLU1197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151C LEU* 3.7 22.2 - - - +
1152C GLY* 4.8 7.9 + - - -
1193C ALA 2.9 18.8 + - - +
1194C GLU* 3.8 11.6 - - - +
1195C ILE 3.2 0.2 - - - -
1196C LYS* 1.3 75.5 - - - +
1198C LEU* 1.3 73.9 + - - +
1200C LYS* 3.5 4.7 + - - +
1201C LEU* 2.9 42.4 + - - +
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Residues in contact with LEU1198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS* 5.3 3.1 - - - -
15C PHE* 4.9 13.5 - - + -
1117C LEU* 5.5 5.4 - - + -
1120C ALA* 4.2 15.1 - - + +
1124C ILE* 3.6 25.7 - - + +
1148C ALA 5.4 0.7 - - - +
1151C LEU* 3.6 35.7 - - + -
1182C ILE* 3.7 30.3 - - + -
1194C GLU 2.9 18.9 + - - +
1195C ILE* 4.0 4.0 - - - +
1197C GLU* 1.3 81.4 + - - +
1199C LEU* 1.3 60.4 + - - +
1201C LEU* 3.0 10.6 + - + +
1202C GLY* 2.9 24.3 + - - -
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Residues in contact with LEU1199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C HIS* 3.2 42.6 - - + +
1119C MET* 4.5 7.2 - - + -
1120C ALA* 3.7 22.0 - - + +
1195C ILE* 2.9 23.2 + - + +
1196C LYS* 4.3 4.3 - - + +
1198C LEU* 1.3 76.4 - - - +
1200C LYS* 1.3 59.5 + - - +
1202C GLY* 3.3 9.2 + - - +
1204C LEU* 3.4 30.7 + - + +
1205C PRO 3.1 30.5 - - - +
1206C THR 4.1 9.9 - - - +
1208C GLY* 4.4 11.7 - - - +
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Residues in contact with LYS1200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196C LYS 2.9 23.0 + - - +
1197C GLU* 3.7 6.5 - - - +
1199C LEU* 1.3 77.9 - - - +
1201C LEU* 1.3 61.6 + - - +
1203C ASP* 3.4 14.0 + - - +
1204C LEU 3.8 10.6 - - - +
1206C THR* 3.3 23.1 - - + +
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Residues in contact with LEU1201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124C ILE* 5.7 2.0 - - + -
1127C LYS* 3.1 18.9 + - - -
1144C PHE* 3.8 28.0 - - + -
1147C ARG* 5.6 6.7 - - + +
1148C ALA* 5.8 2.2 - - - +
1151C LEU* 3.9 32.5 - - + -
1197C GLU* 2.9 28.8 + - - +
1198C LEU* 3.0 15.0 + - + +
1200C LYS* 1.3 73.9 - - - +
1202C GLY* 1.3 57.7 + - - +
1203C ASP* 3.1 7.4 + - - +
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Residues in contact with GLY1202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120C ALA* 5.5 2.2 - - - -
1123C GLY* 4.7 18.2 - - - +
1124C ILE* 5.4 6.1 - - - -
1127C LYS* 4.1 11.4 - - - -
1144C PHE* 5.8 1.3 - - - -
1198C LEU 2.9 12.2 + - - -
1199C LEU* 3.3 5.1 + - - -
1200C LYS 3.2 1.4 - - - -
1201C LEU* 1.3 77.2 - - - +
1203C ASP* 1.3 62.5 + - - +
1204C LEU* 3.0 25.3 + - - +
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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