Contacts of the helix formed by residues 1200 - 1216 (chain 3) in PDB entry 6AH0
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 THR1200 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11943 SER* 5.4 3.4 - - - -
11993 ARG* 1.3 77.0 - - - +
12013 PRO* 1.3 67.3 - - - +
12023 PRO 3.2 2.6 - - - -
12033 GLU* 3.3 6.7 + - - +
12043 VAL* 2.8 22.3 + - - +
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Residues in contact with PRO1201 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11903 GLN 5.4 10.9 - - - +
11913 LYS* 5.7 4.2 - - - -
11943 SER* 5.6 1.0 - - - -
12003 THR* 1.3 70.8 - - - +
12023 PRO* 1.3 56.9 - - - +
12043 VAL* 5.1 0.7 - - - -
12053 SER* 2.9 29.5 + - - -
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Residues in contact with PRO1202 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12003 THR* 3.2 1.4 - - - -
12013 PRO* 1.3 72.1 - - - +
12033 GLU* 1.3 67.9 + - - +
12063 LYS* 3.0 21.9 + - - +
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Residues in contact with GLU1203 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12003 THR* 3.3 11.9 + - - +
12023 PRO* 1.3 75.3 - - - +
12043 VAL* 1.3 62.7 + - - +
12063 LYS* 3.6 0.7 - - - -
12073 LYS* 2.8 20.1 + - - -
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Residues in contact with VAL1204 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11993 ARG* 5.9 0.8 - - - +
12003 THR 2.8 19.7 + - - +
12013 PRO* 3.8 0.7 - - - -
12033 GLU* 1.3 68.6 - - - +
12053 SER* 1.3 54.2 + - - +
12073 LYS* 2.4 29.4 + - - +
12083 LEU* 3.0 9.2 + - - -
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Residues in contact with SER1205 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12013 PRO 2.9 18.4 + - - -
12043 VAL* 1.3 70.3 - - - +
12063 LYS* 1.3 61.9 + - - +
12083 LEU* 3.6 1.9 + - - +
12093 GLU* 3.0 18.2 + - - -
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Residues in contact with LYS1206 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12023 PRO 3.0 16.8 + - - -
12033 GLU 3.6 2.2 - - - -
12043 VAL 2.8 0.8 + - - -
12053 SER* 1.3 76.9 - - - +
12073 LYS* 1.3 53.8 + - - +
12093 GLU* 2.6 23.9 + - - +
12103 ASP* 2.8 11.6 + - - -
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Residues in contact with LYS1207 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12033 GLU 2.8 10.8 + - - -
12043 VAL* 2.4 18.9 + - - +
12063 LYS* 1.3 67.9 - - - +
12083 LEU* 1.3 56.2 + - - +
12103 ASP* 3.5 12.6 + - - +
12113 ILE 4.2 2.4 + - - -
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Residues in contact with LEU1208 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12043 VAL 3.0 8.3 + - - -
12053 SER* 4.0 2.2 - - - +
12063 LYS 3.0 0.8 - - - -
12073 LYS* 1.3 75.8 - - - +
12093 GLU* 1.3 62.4 + - - +
12103 ASP 2.8 5.8 + - - -
12113 ILE* 3.5 9.7 + - - +
12123 ARG* 3.7 8.0 + - - -
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Residues in contact with GLU1209 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12053 SER 3.0 12.5 + - - -
12063 LYS* 2.6 16.7 + - - +
12083 LEU* 1.3 72.1 - - - +
12103 ASP* 1.3 63.6 + - - +
12123 ARG* 5.0 1.1 - - - +
12133 THR* 2.9 18.9 + - - -
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Residues in contact with ASP1210 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12063 LYS 2.8 10.1 + - - -
12073 LYS* 3.5 8.2 + - - +
12083 LEU 2.8 3.6 - - - -
12093 GLU* 1.3 73.2 - - - +
12113 ILE* 1.3 66.3 + - - +
12133 THR* 2.8 14.0 + - - -
12143 ARG* 2.8 13.8 + - - -
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Residues in contact with ILE1211 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12073 LYS 4.2 4.0 + - - -
12083 LEU 3.5 5.8 + - - -
12103 ASP* 1.3 72.5 - - - +
12123 ARG* 1.3 67.9 + - - +
12143 ARG* 3.1 0.8 + - - +
12153 TYR* 2.9 20.8 + - - -
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Residues in contact with ARG1212 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12083 LEU 3.7 9.3 + - - -
12093 GLU* 4.1 2.7 - - - +
12103 ASP 3.2 1.0 - - - -
12113 ILE* 1.3 74.3 - - - +
12133 THR* 1.3 50.7 + - - +
12163 ALA* 2.6 46.3 + - - +
12173 PHE 4.9 6.5 - - - -
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Residues in contact with THR1213 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12093 GLU 2.9 13.0 + - - -
12103 ASP 2.8 11.4 + - - -
12123 ARG* 1.3 75.3 - - - +
12143 ARG* 1.3 64.5 + - - +
12163 ALA 2.8 16.4 + - - +
12173 PHE 5.5 1.3 - - - -
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Residues in contact with ARG1214 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11123 GLY 4.7 0.3 - - - +
11133 GLY* 3.3 24.8 - - - -
11143 SER 3.6 3.2 + - - -
12103 ASP 2.8 15.1 + - - -
12113 ILE* 3.8 1.8 - - - +
12133 THR* 1.3 73.1 - - - +
12153 TYR* 1.3 57.4 + - - +
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Residues in contact with TYR1215 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11093 LEU* 5.1 4.7 + - - -
11103 ILE* 4.6 14.0 + - - -
11133 GLY* 4.8 4.4 - - - -
11143 SER* 4.3 21.1 - - - +
12113 ILE 2.9 12.9 + - - -
12133 THR 3.7 0.4 - - - -
12143 ARG* 1.3 78.1 - - - +
12163 ALA* 1.3 55.7 + - - +
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Residues in contact with ALA1216 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11093 LEU* 6.3 1.1 - - - +
11103 ILE* 6.0 2.5 - - - +
12123 ARG 2.6 31.5 + - - +
12133 THR* 2.8 13.7 + - - +
12153 TYR* 1.3 76.5 - - - +
12173 PHE* 1.3 62.0 + - - +
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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