Contacts of the helix formed by residues 986 - 1002 (chain 1) 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 TYR 986 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9841 GLU 3.6 5.6 - - - +
9851 GLU* 1.3 76.2 - - - +
9871 PRO* 1.3 66.6 - - - +
9881 GLU 3.3 2.6 + - - +
9891 VAL* 3.5 4.1 + - - +
9901 LEU* 3.4 15.1 + - - -
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Residues in contact with PRO 987 (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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9851 GLU 3.4 4.7 - - - +
9861 TYR* 1.3 72.5 - - - +
9881 GLU* 1.3 58.7 + - - +
9891 VAL 2.9 6.2 + - - -
9901 LEU* 3.2 1.5 + - - +
9911 GLY* 2.9 24.1 + - - -
10301 LYS* 6.0 0.4 - - - -
10311 VAL* 5.1 6.9 + - - +
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Residues in contact with GLU 988 (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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9451 ALA 5.9 0.9 - - - -
9491 GLN* 4.1 11.8 - - - -
9861 TYR* 3.3 1.0 - - - +
9871 PRO* 1.3 75.9 - - - +
9891 VAL* 1.3 60.0 + - - +
9911 GLY* 4.4 2.2 - - - -
9921 SER* 4.3 5.4 + - - -
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Residues in contact with VAL 989 (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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9451 ALA 5.4 5.7 + - - -
9491 GLN* 4.4 16.5 - - - +
9861 TYR* 3.5 6.3 + - - +
9871 PRO 3.0 0.8 - - - -
9881 GLU* 1.3 75.6 - - - +
9901 LEU* 1.3 67.6 + - - +
9911 GLY 2.8 3.3 + - - -
9921 SER* 2.8 15.8 + - - -
9931 ILE* 2.9 8.6 + - - -
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Residues in contact with LEU 990 (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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9811 TYR 5.6 5.6 - - - -
9821 LEU* 6.0 4.5 - - - +
9841 GLU* 5.1 9.2 + - - +
9861 TYR 3.4 11.0 + - - -
9871 PRO* 3.2 5.2 + - - -
9891 VAL* 1.3 71.3 - - - +
9911 GLY* 1.3 62.5 + - - +
9931 ILE* 3.0 4.1 + - - +
9941 LEU* 2.9 21.0 + - - -
10311 VAL* 5.7 1.1 - - - -
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Residues in contact with GLY 991 (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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9871 PRO 2.9 15.6 + - - -
9881 GLU* 5.0 1.1 - - - -
9891 VAL 2.8 4.8 + - - -
9901 LEU* 1.3 75.2 - - - +
9921 SER* 1.3 63.4 + - - -
9931 ILE 3.0 0.2 + - - -
9941 LEU* 3.0 1.4 + - - -
9951 GLY* 3.0 17.5 + - - -
10301 LYS* 4.4 24.7 - - - -
10311 VAL* 4.5 5.0 - - - +
10341 ASN* 5.4 6.1 - - - -
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Residues in contact with SER 992 (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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9491 GLN* 4.8 12.6 - - - +
9521 ALA* 4.6 13.8 - - - -
9531 ASP* 4.7 5.4 + - - +
9881 GLU 4.3 6.0 + - - -
9891 VAL 2.8 10.4 + - - -
9911 GLY* 1.3 71.3 - - - -
9931 ILE* 1.3 65.1 + - - +
9951 GLY* 3.2 3.2 + - - +
9961 ALA* 2.9 17.2 + - - -
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Residues in contact with ILE 993 (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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9491 GLN* 5.9 0.2 - - - +
9521 ALA* 5.4 6.0 - - - +
9891 VAL 2.9 12.1 + - - -
9901 LEU* 3.0 7.2 + - - +
9911 GLY 3.0 0.4 + - - -
9921 SER* 1.3 72.4 - - - +
9941 LEU* 1.3 69.8 + - - +
9961 ALA* 2.9 12.6 + - - -
9971 LEU 2.9 7.4 + - - -
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Residues in contact with LEU 994 (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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9901 LEU 2.9 16.2 + - - -
9911 GLY 3.6 2.2 - - - -
9931 ILE* 1.3 69.0 - - - +
9951 GLY* 1.3 54.3 + - - +
9971 LEU* 2.2 30.9 + - - +
9981 LYS 2.8 10.6 + - - -
10341 ASN 5.7 9.0 - - - -
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Residues in contact with GLY 995 (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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9561 SER* 5.0 4.4 - - - -
9911 GLY 3.0 13.2 + - - -
9921 SER* 3.6 5.2 - - - -
9941 LEU* 1.3 74.3 - - - +
9961 ALA* 1.3 64.5 + - - +
9981 LYS* 3.0 2.8 + - - -
9991 ALA* 3.0 19.4 + - - -
10341 ASN* 5.4 8.1 - - - +
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Residues in contact with ALA 996 (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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9521 ALA 4.9 3.8 + - - -
9531 ASP* 6.0 0.4 - - - +
9551 ILE* 5.1 1.3 - - - +
9561 SER* 4.1 24.7 - - - +
9921 SER 2.9 9.1 + - - -
9931 ILE 2.9 8.9 + - - -
9951 GLY* 1.3 76.4 - - - +
9971 LEU* 1.3 62.9 + - - +
9991 ALA* 3.3 1.4 + - - -
10001 ILE* 2.9 19.6 + - - -
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Residues in contact with LEU 997 (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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9931 ILE 2.9 7.4 + - - -
9941 LEU* 2.2 20.6 + - - +
9961 ALA* 1.3 67.1 - - - +
9981 LYS* 1.3 64.8 + - - +
10001 ILE* 2.7 14.4 + - - +
10011 VAL* 2.8 9.0 + - - -
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Residues in contact with LYS 998 (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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9941 LEU 2.8 14.5 + - - -
9951 GLY* 3.0 3.8 + - - -
9971 LEU* 1.3 67.8 - - - +
9991 ALA* 1.3 54.5 + - - +
10011 VAL* 2.5 27.5 + - - +
10021 ASN* 3.1 8.7 + - - -
10381 LEU* 5.6 10.1 - - - +
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Residues in contact with ALA 999 (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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9561 SER 4.9 13.0 - - - -
9591 ALA* 5.1 9.6 - - - -
9601 VAL 5.7 0.2 + - - -
9951 GLY 3.0 13.3 + - - -
9961 ALA 3.7 2.5 - - - -
9981 LYS* 1.3 73.5 - - - +
10001 ILE* 1.3 61.2 + - - +
10021 ASN* 3.5 10.9 + - - +
10031 VAL* 3.6 7.4 + - - -
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Residues in contact with ILE1000 (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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9591 ALA* 5.8 4.3 - - - +
9961 ALA 2.9 10.5 + - - -
9971 LEU* 2.7 14.3 + - - +
9991 ALA* 1.3 73.3 - - - +
10011 VAL* 1.3 60.9 + - - +
10031 VAL* 3.3 1.4 + - - -
10041 ILE* 3.2 20.1 + - - +
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Residues in contact with VAL1001 (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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9971 LEU 2.8 6.9 + - - -
9981 LYS* 2.5 15.9 + - - +
10001 ILE* 1.3 73.3 - - - +
10021 ASN* 1.3 55.0 + - - +
10031 VAL 2.8 4.0 + - - -
10041 ILE 2.6 26.3 - - - +
10051 GLY* 4.5 1.7 - - - -
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Residues in contact with ASN1002 (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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9981 LYS 3.1 9.7 + - - -
9991 ALA* 3.5 7.3 + - - +
10001 ILE 3.3 0.6 - - - -
10011 VAL* 1.3 74.2 - - - +
10031 VAL* 1.3 57.0 + - - +
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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