Contacts of the helix formed by residues 209 - 216 (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 GLY 209 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2081 PRO* 1.3 69.1 - - - +
2101 ALA* 1.3 67.6 + - - +
2121 PRO* 3.7 5.8 - - - -
2131 LYS* 2.9 14.9 + - - -
6471 PHE 5.7 0.3 - - - +
6501 ALA* 5.2 14.9 - - - -
6511 VAL* 5.6 3.1 - - - -
6541 SER* 5.8 6.4 - - - +
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Residues in contact with ALA 210 (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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2071 THR 4.7 3.1 - - - -
2081 PRO 2.7 4.4 + - - -
2091 GLY* 1.3 74.1 - - - +
2111 THR* 1.3 56.0 + - - +
2131 LYS* 2.5 27.2 + - - -
2141 LYS* 2.9 9.1 + - - -
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Residues in contact with THR 211 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2071 THR 4.3 6.0 + - - -
2081 PRO 2.6 14.3 + - - -
2101 ALA* 1.3 69.6 - - - +
2121 PRO* 1.3 55.0 - - - +
2141 LYS* 3.3 3.4 + - - +
2151 LEU* 3.0 23.9 + - - -
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Residues in contact with PRO 212 (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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2081 PRO 3.3 8.2 - - - +
2091 GLY* 3.5 6.5 - - - +
2101 ALA 2.7 2.0 - - - -
2111 THR* 1.3 77.1 - - - +
2131 LYS* 1.4 58.9 + - - +
2151 LEU* 4.5 1.3 - - - +
2161 SER* 2.9 27.7 + - - -
6461 PRO 4.8 2.4 - - - +
6501 ALA* 5.0 14.7 - - - +
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Residues in contact with LYS 213 (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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2091 GLY 2.9 11.4 + - - -
2101 ALA* 2.5 14.8 + - - +
2121 PRO* 1.4 73.6 - - - +
2141 LYS* 1.4 62.5 + - - +
2161 SER* 3.6 6.5 + - - +
2171 SER 4.2 1.6 + - - -
6461 PRO 4.9 12.5 - - - -
6471 PHE* 5.3 5.6 - - - +
6501 ALA* 5.4 0.4 - - - +
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Residues in contact with LYS 214 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101 ALA 2.9 10.2 + - - -
2111 THR* 3.3 5.6 + - - +
2121 PRO 3.1 0.2 - - - -
2131 LYS* 1.4 76.3 - - - +
2151 LEU* 1.3 53.8 + - - +
2161 SER 2.7 14.5 + - - -
2171 SER* 3.1 9.5 + - - -
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Residues in contact with LEU 215 (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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2111 THR 3.0 16.3 + - - -
2121 PRO* 3.9 1.3 - - - -
2141 LYS* 1.3 70.5 - - - +
2161 SER* 1.3 56.3 + - - +
2171 SER 2.9 2.2 - - - -
2181 TRP* 2.9 24.1 + - - -
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Residues in contact with SER 216 (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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2121 PRO 2.9 19.4 + - - -
2131 LYS* 4.0 5.4 - - - +
2141 LYS 2.7 2.8 + - - -
2151 LEU* 1.3 76.9 - - - +
2171 SER* 1.3 56.7 + - - +
2181 TRP 3.2 2.5 + - - -
2191 ASP 4.7 3.2 + - - -
6461 PRO* 4.9 17.0 - - - +
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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