Contacts of the helix formed by residues 1165 - 1178 (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 TYR1165 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11611 MET 4.5 2.2 + - - -
11621 GLY* 3.4 5.3 + - - -
11641 ASP* 1.3 72.5 - - - +
11661 ILE* 1.3 64.8 + - - +
11671 TYR 3.0 1.1 - - - -
11681 ALA* 2.7 17.4 + - - +
11691 VAL 3.2 7.6 + - - -
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Residues in contact with ILE1166 (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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11621 GLY* 3.4 12.5 + - - -
11631 LYS 5.6 0.2 - - - -
11641 ASP 2.6 10.0 + - - -
11651 TYR* 1.3 73.2 - - - +
11671 TYR* 1.3 61.4 + - - +
11691 VAL* 3.0 2.4 + - - -
11701 THR* 2.9 21.0 + - - -
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Residues in contact with TYR1167 (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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11641 ASP 3.3 7.4 + - - -
11651 TYR 3.0 1.4 - - - -
11661 ILE* 1.3 73.9 - - - +
11681 ALA* 1.3 65.8 + - - +
11701 THR* 3.2 12.0 + - - +
11711 PRO 4.1 4.0 - - - -
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Residues in contact with ALA1168 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11651 TYR* 2.7 17.2 + - - +
11671 TYR* 1.3 73.5 - - - +
11691 VAL* 1.3 62.5 + - - +
11711 PRO 4.2 3.1 - - - -
11721 LEU* 4.3 3.3 + - - -
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Residues in contact with VAL1169 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11651 TYR 3.2 6.0 + - - -
11661 ILE 3.0 6.6 + - - -
11681 ALA* 1.3 75.0 - - - +
11701 THR* 1.3 56.5 + - - +
11721 LEU* 2.5 30.9 + - - +
11731 LEU* 2.8 10.7 + - - -
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Residues in contact with THR1170 (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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11661 ILE 2.9 14.4 + - - -
11671 TYR* 3.2 6.6 + - - +
11691 VAL* 1.3 73.9 - - - +
11711 PRO* 1.3 64.2 - - - +
11731 LEU* 3.1 3.6 + - - +
11741 GLU* 2.9 17.7 + - - -
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Residues in contact with PRO1171 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11671 TYR 4.1 6.1 - - - -
11681 ALA 4.2 1.8 - - - +
11691 VAL 3.0 2.0 - - - -
11701 THR* 1.3 73.1 - - - +
11721 LEU* 1.3 59.0 + - - +
11741 GLU* 2.7 18.9 + - - +
11751 ASP* 2.9 10.7 + - - -
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Residues in contact with LEU1172 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11681 ALA 4.3 3.8 + - - -
11691 VAL* 2.5 15.0 + - - +
11711 PRO* 1.3 71.1 - - - +
11731 LEU* 1.3 60.8 - - - +
11751 ASP* 2.8 14.3 + - - +
11761 ALA* 2.9 13.0 + - - -
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Residues in contact with LEU1173 (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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11691 VAL 2.8 16.0 + - - -
11701 THR* 3.1 5.1 + - - +
11721 LEU* 1.3 71.0 - - - +
11741 GLU* 1.3 56.7 + - - +
11761 ALA* 4.6 0.9 - - - +
11771 LEU* 2.8 29.3 + - - +
11881 ALA* 6.3 2.7 - - - +
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Residues in contact with GLU1174 (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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11701 THR 2.9 9.2 + - - -
11711 PRO* 2.7 17.5 + - - -
11731 LEU* 1.3 72.1 - - - +
11751 ASP* 1.3 55.7 + - - +
11771 LEU* 5.1 0.2 - - - +
11781 MET* 2.9 24.6 + - - -
12141 TYR* 6.4 1.8 - - - +
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Residues in contact with ASP1175 (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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11711 PRO 2.9 8.0 + - - -
11721 LEU* 2.8 8.4 + - - +
11741 GLU* 1.3 73.4 - - - +
11761 ALA* 1.3 52.3 + - - +
11771 LEU 3.1 0.5 + - - -
11781 MET* 2.6 33.4 + - - +
11791 ASP 4.8 0.9 - - - +
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Residues in contact with ALA1176 (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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11721 LEU 2.9 14.8 + - - -
11731 LEU* 4.3 1.3 - - - +
11751 ASP* 1.3 71.6 - - - +
11771 LEU* 1.3 56.2 + - - +
11781 MET 2.6 15.2 - - - +
11791 ASP* 4.6 0.5 - - - -
11801 ARG 4.7 1.7 + - - -
11841 HIS* 3.9 26.5 - - - +
11851 ARG 4.1 0.5 + - - -
11881 ALA* 6.2 1.1 - - - -
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Residues in contact with LEU1177 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11731 LEU* 2.8 20.2 + - - +
11741 GLU 3.9 0.2 - - - -
11761 ALA* 1.3 74.9 - - - +
11781 MET* 1.3 64.9 + - - +
11791 ASP* 3.4 2.6 + - - -
11841 HIS 5.0 0.7 - - - -
11851 ARG* 4.5 16.8 - - - +
11881 ALA* 6.1 3.5 - - - +
12141 TYR 4.9 13.2 - - - +
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Residues in contact with MET1178 (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 2.9 14.9 + - - -
11751 ASP 2.6 14.2 - - - +
11761 ALA* 2.6 22.9 - - - +
11771 LEU* 1.3 73.9 - - - +
11791 ASP* 1.3 66.0 + - - +
11801 ARG 3.4 0.3 + - - -
12141 TYR* 5.3 2.0 + - - +
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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