Contacts of the helix formed by residues 2189 - 2203 (chain A) 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 SER2189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2187A GLN 3.4 6.0 + - - -
2188A LEU* 1.3 71.7 - - - +
2190A PRO* 1.3 56.7 - - - +
2191A GLN 3.0 3.8 - - - +
2192A ASP* 2.5 32.7 + - - +
2193A VAL 3.2 5.2 + - - -
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Residues in contact with PRO2190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2188A LEU 3.4 4.1 - - - +
2189A SER* 1.3 69.0 - - - +
2191A GLN* 1.3 61.7 + - - +
2193A VAL* 4.6 2.0 - - - +
2194A THR* 2.9 23.4 + - - -
2246A ASN 5.9 2.3 - - - +
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Residues in contact with GLN2191 (chain A).
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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2155A GLN 5.6 6.1 - - - -
2189A SER 2.9 1.6 + - - -
2190A PRO* 1.3 75.3 - - - +
2192A ASP* 1.3 56.4 + - - +
2194A THR* 4.1 0.6 - - - +
2195A THR* 2.9 23.7 + - - -
2244A LYS* 5.4 11.5 + - - +
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Residues in contact with ASP2192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189A SER* 2.5 18.6 + - - +
2191A GLN* 1.3 67.3 - - - +
2193A VAL* 1.3 65.7 + - - +
2194A THR 3.0 0.9 - - - -
2195A THR* 2.8 13.4 + - - +
2196A HIS* 2.8 13.0 + - - -
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Residues in contact with VAL2193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2188A LEU* 5.2 2.2 + - - +
2189A SER 3.2 9.7 + - - -
2190A PRO* 3.4 2.6 + - - -
2192A ASP* 1.3 71.0 - - - +
2194A THR* 1.3 57.6 + - - +
2196A HIS* 4.6 1.6 - - - +
2197A ALA* 2.9 27.4 + - - -
2234A GLY 5.2 4.3 - - - +
2238A GLY* 4.3 6.8 - - - -
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Residues in contact with THR2194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2190A PRO 2.9 16.4 + - - -
2191A GLN* 4.1 1.1 - - - +
2193A VAL* 1.3 77.9 - - - +
2195A THR* 1.3 61.0 + - - +
2197A ALA* 3.9 0.5 - - - -
2198A LYS* 3.0 21.3 + - - -
2238A GLY* 4.0 23.7 - - - +
2241A ASN* 6.1 0.7 - - - +
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Residues in contact with THR2195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2191A GLN 2.9 14.2 + - - -
2192A ASP* 2.8 12.5 + - - +
2194A THR* 1.3 70.3 - - - +
2196A HIS* 1.3 55.5 + - - +
2198A LYS* 3.2 2.8 + - - +
2199A ILE* 2.9 25.1 + - - -
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Residues in contact with HIS2196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192A ASP 2.8 13.7 + - - -
2193A VAL* 3.9 1.8 - - - +
2195A THR* 1.3 73.2 - - - +
2197A ALA* 1.3 65.9 + - - +
2199A ILE* 3.1 3.7 + - - +
2200A MET* 2.9 19.6 + - - -
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Residues in contact with ALA2197 (chain A).
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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2193A VAL 2.9 16.5 + - - -
2194A THR 3.9 0.7 - - - -
2196A HIS* 1.3 73.9 - - - +
2198A LYS* 1.3 57.2 + - - +
2200A MET* 2.9 4.3 + - - +
2201A ALA* 2.8 27.0 + - - -
2235A TYR* 4.6 21.8 - - - +
2238A GLY 4.8 0.4 - - - -
2239A ARG* 4.7 10.6 - - - +
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Residues in contact with LYS2198 (chain A).
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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2194A THR 3.0 15.0 + - - -
2195A THR 3.6 4.3 - - - -
2196A HIS 3.2 0.2 - - - -
2197A ALA* 1.3 74.1 - - - +
2199A ILE* 1.3 63.4 + - - +
2201A ALA* 3.9 2.5 - - - +
2202A ASP* 3.7 12.1 + - - -
2238A GLY 4.7 5.6 + - - -
2239A ARG* 5.2 4.5 - - - +
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Residues in contact with ILE2199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195A THR 2.9 13.2 + - - -
2196A HIS* 3.1 4.2 + - - +
2198A LYS* 1.3 76.2 - - - +
2200A MET* 1.3 52.7 + - - +
2201A ALA 3.1 0.2 - - - -
2202A ASP* 3.1 3.1 + - - -
2203A ASN* 2.6 34.7 + - - -
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Residues in contact with MET2200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196A HIS 2.9 10.0 + - - -
2197A ALA* 2.9 8.3 + - - +
2199A ILE* 1.3 74.8 - - - +
2201A ALA* 1.3 64.4 - - - +
2203A ASN 3.1 23.3 - - - +
2204A PRO* 4.9 0.7 - - - +
2206A TRP* 4.9 7.0 - - - +
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Residues in contact with ALA2201 (chain A).
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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2197A ALA 2.8 12.7 + - - -
2198A LYS* 3.8 3.1 + - - +
2199A ILE 3.1 0.4 - - - -
2200A MET* 1.3 80.5 - - - +
2202A ASP* 1.3 59.5 + - - +
2203A ASN* 4.6 1.0 - - - -
2204A PRO 5.1 0.3 - - - -
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Residues in contact with ASP2202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2198A LYS 3.7 9.1 + - - -
2199A ILE 3.1 6.5 + - - -
2201A ALA* 1.3 78.4 - - - +
2203A ASN* 1.3 55.8 + - - +
2204A PRO 4.2 1.3 - - - -
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Residues in contact with ASN2203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2199A ILE 2.6 18.1 + - - -
2200A MET* 3.1 20.0 - - - +
2201A ALA 3.3 1.5 - - - -
2202A ASP* 1.3 75.4 - - - +
2204A PRO* 1.3 62.6 - - - +
2205A SER* 3.1 3.6 - - - +
2206A TRP* 3.2 19.8 + - - +
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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