Contacts of the helix formed by residues 1204 - 1216 (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 CYS1204 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12021 PHE 3.7 2.0 - - - -
12031 GLY* 1.3 76.0 - - - +
12051 GLU* 1.3 66.0 + - - +
12061 ASP 2.9 4.3 + - - -
12071 SER* 3.5 8.8 + - - -
12081 LEU 3.9 3.6 + - - -
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Residues in contact with GLU1205 (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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12031 GLY* 3.2 6.5 + - - -
12041 CYS* 1.3 75.4 - - - +
12061 ASP* 1.3 53.3 + - - +
12081 LEU* 2.4 30.9 + - - +
12091 ASN 2.8 9.9 + - - -
12401 ALA 5.5 8.1 - - - -
12411 ILE* 5.9 4.3 - - - +
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Residues in contact with ASP1206 (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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12031 GLY 4.9 1.6 + - - -
12041 CYS 2.9 4.4 + - - -
12051 GLU* 1.3 73.2 - - - +
12071 SER* 1.3 63.3 + - - +
12091 ASN* 3.0 4.8 + - - +
12101 HIS* 3.0 15.4 + - - -
5852 THR 5.2 1.4 - - - +
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Residues in contact with SER1207 (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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12041 CYS 3.5 6.5 + - - -
12051 GLU 3.3 0.2 - - - -
12061 ASP* 1.3 71.2 - - - +
12081 LEU* 1.3 56.0 + - - +
12101 HIS* 2.4 26.7 + - - +
12111 LEU 2.9 10.9 + - - -
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Residues in contact with LEU1208 (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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12041 CYS 3.9 3.2 + - - -
12051 GLU* 2.4 20.0 + - - +
12071 SER* 1.3 68.1 - - - +
12091 ASN* 1.3 60.2 + - - +
12111 LEU* 3.4 3.7 + - - +
12121 LEU* 2.9 20.1 + - - -
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Residues in contact with ASN1209 (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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12051 GLU 2.8 10.9 + - - -
12061 ASP* 3.0 5.1 + - - +
12081 LEU* 1.3 74.4 - - - +
12101 HIS* 1.3 64.4 + - - +
12121 LEU* 2.8 16.8 + - - +
12131 ASN 3.5 2.9 + - - -
5862 ILE 5.7 1.6 - - - -
5872 HIS* 6.6 0.2 - - - -
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Residues in contact with HIS1210 (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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12061 ASP 3.0 7.6 + - - -
12071 SER* 2.4 16.1 + - - +
12091 ASN* 1.3 72.4 - - - +
12111 LEU* 1.3 62.2 + - - +
12121 LEU 3.1 0.2 + - - -
12131 ASN* 3.1 12.3 + - - -
12141 TYR 4.0 2.1 + - - -
5852 THR* 3.7 28.6 + - - +
5862 ILE 5.0 3.1 + - - -
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Residues in contact with LEU1211 (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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12071 SER 2.9 13.7 + - - -
12081 LEU* 3.8 3.8 - - - +
12101 HIS* 1.3 72.0 - - - +
12121 LEU* 1.3 64.4 + - - +
12141 TYR* 2.9 15.8 + - - +
12151 VAL* 3.0 9.2 + - - -
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Residues in contact with LEU1212 (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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12081 LEU 2.9 10.6 + - - -
12091 ASN* 2.8 12.6 + - - +
12111 LEU* 1.3 73.9 - - - +
12131 ASN* 1.3 66.7 - - - +
12151 VAL* 3.1 3.3 + - - +
12161 TRP* 2.9 18.7 + - - -
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Residues in contact with ASN1213 (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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12091 ASN 3.5 4.6 + - - -
12101 HIS 3.1 9.0 + - - -
12111 LEU 2.9 1.6 + - - -
12121 LEU* 1.3 73.0 - - - +
12141 TYR* 1.3 54.7 + - - +
12151 VAL 3.3 0.2 - - - -
12161 TRP* 2.6 29.6 + - - +
12171 PRO 4.1 2.6 - - - -
5892 ASP 5.1 4.0 - - - -
5902 LEU* 4.8 15.2 - - - +
5912 TYR 4.7 11.5 + - - +
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Residues in contact with TYR1214 (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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11741 GLU* 6.4 1.8 - - - +
11771 LEU* 4.9 14.9 - - - +
11781 MET* 5.9 0.3 - - - -
12101 HIS 4.0 2.8 + - - -
12111 LEU* 2.9 10.7 + - - +
12131 ASN* 1.3 70.0 - - - +
12151 VAL* 1.3 61.6 + - - +
12171 PRO 4.7 1.6 - - - -
5912 TYR* 5.1 7.8 - - - +
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Residues in contact with VAL1215 (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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12111 LEU 3.0 10.3 + - - -
12121 LEU* 3.5 4.5 - - - +
12131 ASN 2.7 2.8 + - - -
12141 TYR* 1.3 79.5 - - - +
12161 TRP* 1.3 64.6 + - - +
12171 PRO 3.0 0.2 - - - -
12181 ASN* 2.8 18.2 + - - -
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Residues in contact with TRP1216 (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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12121 LEU 2.9 9.3 + - - -
12131 ASN* 2.6 17.5 + - - +
12151 VAL* 1.3 70.2 - - - +
12171 PRO* 1.3 52.0 - - - +
12181 ASN 2.7 12.8 + - - -
12191 VAL* 2.9 14.6 + - - -
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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