Contacts of the helix formed by residues 1012 - 1023 (chain C) in PDB entry 6AU8
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 TRP1012 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A TRP* 5.4 4.7 - + - -
242A PHE* 3.5 64.5 - + + -
245A LEU* 3.7 33.3 - - + +
246A ALA* 4.6 2.9 - - + -
251A LYS* 5.3 5.6 - - - -
254A VAL* 3.4 30.1 - - + -
258A LEU* 4.2 4.3 - - + -
1008C VAL* 4.0 9.9 - - + -
1009C PRO* 3.0 48.1 + - + +
1011C GLU* 1.3 88.5 - - + +
1013C VAL* 1.3 65.7 + - - +
1014C PRO* 3.5 0.7 - - - -
1015C ILE* 3.2 6.1 + - + +
1016C ILE* 3.0 39.5 + - + +
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Residues in contact with VAL1013 (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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1004C TRP* 3.7 17.5 - - + -
1005C ALA* 4.0 24.0 - - + +
1008C VAL* 4.0 14.4 - - + -
1009C PRO 3.9 9.9 - - - +
1010C PRO* 3.1 22.2 + - + +
1012C TRP* 1.3 77.6 - - - +
1014C PRO* 1.4 62.1 - - + +
1016C ILE 3.3 0.3 + - - -
1017C GLN* 2.9 47.8 + - - +
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Residues in contact with PRO1014 (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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1010C PRO 3.7 6.1 - - - +
1011C GLU* 3.6 12.1 - - - +
1012C TRP 3.6 2.0 - - - -
1013C VAL* 1.4 94.7 - - + +
1015C ILE* 1.3 64.7 + - + +
1017C GLN* 3.4 16.1 - - - +
1018C GLN* 2.9 42.1 + - - +
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Residues in contact with ILE1015 (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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231A PRO* 3.9 30.1 - - + -
238A ASN* 3.6 28.7 - - - +
241A TRP* 4.1 16.6 - - + -
242A PHE* 3.8 20.6 - - + -
1011C GLU 3.7 21.1 - - - +
1012C TRP* 3.2 7.3 + - + +
1014C PRO* 1.3 78.2 - - + +
1016C ILE* 1.3 58.7 + - - +
1018C GLN* 3.2 13.1 + - - +
1019C ASP* 3.0 32.5 + - - +
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Residues in contact with ILE1016 (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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242A PHE* 3.7 20.9 - - + -
257A VAL* 5.7 1.6 - - + -
258A LEU* 4.2 17.7 - - + -
261A GLN* 4.3 13.5 - - + -
262A TYR* 3.7 16.4 - - + +
1004C TRP* 3.4 37.0 - - + -
1008C VAL* 4.4 7.9 - - + -
1012C TRP* 3.0 35.9 + - + +
1015C ILE* 1.3 73.3 - - - +
1017C GLN* 1.3 55.1 + - - +
1019C ASP* 3.2 1.0 + - - +
1020C ILE* 2.8 47.6 + - + +
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Residues in contact with GLN1017 (chain C).
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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1002C GLU* 6.1 3.0 - - - +
1004C TRP* 4.0 15.8 - - + -
1013C VAL* 2.9 29.3 + - - +
1014C PRO* 3.4 22.3 - - - +
1016C ILE* 1.3 77.3 - - - +
1018C GLN* 1.3 62.9 + - + +
1020C ILE* 3.3 9.7 + - - +
1021C GLN* 3.2 26.3 + - - +
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Residues in contact with GLN1018 (chain C).
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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1014C PRO* 2.9 36.4 + - - +
1015C ILE* 3.6 11.1 - - - +
1017C GLN* 1.3 78.0 - - + +
1019C ASP* 1.3 61.9 + - - +
1021C GLN* 3.1 8.3 + - - +
1022C SER* 2.8 34.7 + - - +
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Residues in contact with ASP1019 (chain C).
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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232A PHE 4.8 0.7 - - - +
233A VAL 4.6 3.8 - - - +
235A PRO* 3.8 20.7 - - + +
238A ASN* 2.9 32.9 + - - +
262A TYR* 2.6 40.4 + - + +
1015C ILE* 3.0 19.9 + - - +
1016C ILE 3.2 3.1 + - - +
1018C GLN* 1.3 77.8 - - - +
1020C ILE* 1.3 67.1 + - + +
1022C SER* 3.8 6.3 + - - -
1023C GLN* 3.0 32.5 + - - +
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Residues in contact with ILE1020 (chain C).
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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261A GLN* 3.2 39.5 - - + +
262A TYR* 6.4 0.2 - - + -
1004C TRP* 3.6 32.8 - - + +
1016C ILE* 2.8 32.1 + - + +
1017C GLN* 3.6 6.3 - - - +
1019C ASP* 1.3 75.3 - - + +
1021C GLN* 1.3 75.6 + - - +
1023C GLN* 3.5 14.0 + - - +
1024C ARG* 3.5 17.4 + - + +
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Residues in contact with GLN1021 (chain C).
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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1017C GLN* 3.2 13.5 + - + +
1018C GLN* 3.1 10.6 + - - +
1020C ILE* 1.3 83.7 - - - +
1022C SER* 1.3 65.2 + - - +
1024C ARG* 3.0 58.4 + - - +
1025C LYS* 3.9 5.6 + - - +
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Residues in contact with SER1022 (chain C).
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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233A VAL 5.5 1.8 + - - -
235A PRO* 4.2 18.8 - - - -
1018C GLN* 2.8 25.6 + - - +
1019C ASP* 3.4 6.9 + - - -
1021C GLN* 1.3 71.3 - - - +
1023C GLN* 1.3 57.5 + - - +
1025C LYS* 3.1 45.9 + - - +
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Residues in contact with GLN1023 (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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235A PRO* 4.2 10.3 - - + -
261A GLN 3.1 22.0 + - - -
262A TYR* 3.4 23.1 - - - +
264A PRO* 3.4 33.5 - - + +
265A SER* 2.9 44.2 + - - +
1019C ASP 3.0 31.3 + - - +
1020C ILE* 3.8 7.2 - - - +
1021C GLN 3.2 0.2 - - - -
1022C SER* 1.3 73.0 - - - +
1024C ARG* 1.3 63.0 + - - +
1025C LYS 3.2 6.9 - - - +
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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