Contacts of the helix formed by residues 116 - 123 (chain 1) in PDB entry 1AR9
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 VAL 116 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151 THR* 1.3 79.4 - - - +
1171 GLN* 1.3 73.7 + - + +
1181 LEU 3.6 0.9 - - - -
1191 ARG* 3.5 4.6 + - - +
1201 ARG* 3.0 30.8 + - - +
2791 TYR* 3.8 33.0 - - + +
2313 ILE* 4.2 11.2 - - + -
2323 GLU* 3.9 19.5 - - - +
2333 GLN* 3.0 46.1 + - + +
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Residues in contact with GLN 117 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 ALA* 5.9 5.8 - - + +
1151 THR* 4.0 2.4 + - - -
1161 VAL* 1.3 88.4 - - + +
1181 LEU* 1.3 62.6 + - - +
1201 ARG* 3.3 5.4 + - - +
1211 LYS* 3.2 27.3 + - + +
1063 TYR* 4.9 2.7 + - + -
2273 ASP* 3.5 40.2 + - - +
2283 THR* 5.3 3.8 - - + +
2313 ILE* 4.7 13.6 - - + +
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Residues in contact with LEU 118 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 PHE* 4.4 17.3 - - + +
831 ARG 5.9 1.1 - - - +
851 ALA* 3.7 27.3 - - + +
861 CYS 5.6 0.4 + - - +
871 VAL* 4.0 23.8 - - + -
1121 TYR* 4.3 8.3 - - + +
1151 THR* 5.2 4.8 + - - +
1161 VAL 5.2 0.2 - - - +
1171 GLN* 1.3 75.8 - - - +
1191 ARG* 1.3 65.0 + - - +
1211 LYS* 3.0 12.8 + - + +
1221 LEU* 2.9 44.8 + - + +
2611 LEU* 4.0 33.2 - - + +
2631 PRO* 4.5 10.8 - - + -
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Residues in contact with ARG 119 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121 TYR* 3.6 34.6 + - + +
1131 LYS* 3.8 38.3 + - - +
1151 THR* 3.8 8.6 + - - +
1161 VAL* 3.5 9.5 + - - +
1171 GLN 3.3 0.4 - - - -
1181 LEU* 1.3 77.1 - - - +
1201 ARG* 1.3 56.5 + - - +
1221 LEU* 3.3 1.4 + - - +
1231 GLU* 2.9 60.9 + - - +
2791 TYR* 3.2 42.8 - - - +
2811 GLY 3.0 18.8 + - - -
2821 PRO 3.2 15.6 + - - -
2831 GLY 3.0 27.3 + - - -
2841 VAL* 6.0 0.2 - - - +
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Residues in contact with ARG 120 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 VAL 3.0 16.9 + - - +
1171 GLN 3.7 4.3 - - - +
1191 ARG* 1.3 75.1 - - - +
1211 LYS* 1.4 63.5 + - - +
1231 GLU* 3.2 11.3 + - - +
1241 PHE* 3.4 13.7 + - - -
2741 PRO* 3.7 16.5 - - + +
2751 ARG* 2.9 39.1 + - + +
2761 ALA* 4.9 2.0 - - - +
2791 TYR* 3.2 19.7 + - + +
1023 GLU* 2.9 32.5 + - - -
1063 TYR* 2.9 37.7 + - - +
2283 THR* 3.6 10.7 + - - +
2303 HIS* 3.7 16.5 + - - +
2313 ILE* 3.5 28.9 - - + +
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Residues in contact with LYS 121 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801 PHE* 2.9 51.8 + - + -
811 PHE* 3.6 30.0 - - + +
831 ARG* 4.9 9.7 - - - +
1171 GLN* 3.2 13.6 + - + +
1181 LEU* 3.0 16.5 + - + +
1201 ARG* 1.4 75.9 - - - +
1221 LEU* 1.3 63.1 + - - +
1241 PHE* 3.1 29.4 + - - +
1063 TYR* 3.6 32.1 - - + -
2253 LEU* 4.3 13.9 - - - +
2273 ASP* 5.5 4.5 - - - +
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Residues in contact with LEU 122 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811 PHE* 3.6 25.1 - - + -
1121 TYR* 3.7 46.4 - - + -
1181 LEU* 2.9 37.0 + - + +
1191 ARG 3.8 2.9 - - - +
1211 LYS* 1.3 71.7 - - - +
1231 GLU* 1.3 58.6 + - - +
1251 PHE* 3.0 17.0 + - - +
1301 PHE* 4.3 24.2 - - + -
2071 HIS* 2.8 41.2 + - + +
2611 LEU* 6.0 0.9 - - + -
2631 PRO* 4.7 5.2 - - + -
2661 ILE* 4.4 8.5 - - + -
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Residues in contact with GLU 123 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121 TYR* 4.2 9.3 - - + -
1131 LYS* 4.2 6.2 - - - -
1191 ARG* 2.9 42.8 + - + +
1201 ARG* 3.7 6.7 - - + +
1211 LYS 3.2 0.6 - - - -
1221 LEU* 1.3 77.4 - - + +
1241 PHE* 1.3 57.7 + - - +
1251 PHE 2.9 11.3 + - - +
2071 HIS* 4.5 10.9 - - + +
2081 PHE* 3.7 32.0 - - + -
2721 ARG* 3.7 19.1 - - - +
2731 PRO 4.3 6.4 - - - +
2741 PRO* 5.0 2.3 - - - +
2751 ARG* 5.0 5.6 - - - +
2791 TYR* 2.8 36.5 + - - +
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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