Contacts of the helix formed by residues 2231 - 2241 (chain A) in PDB entry 6FF7
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 THR2231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2230A LEU* 1.3 75.7 - - - +
2232A PRO* 1.3 53.2 - - - +
2233A SER* 4.5 3.6 - - - -
2234A GLY* 3.2 6.1 + - - -
2235A TYR* 2.7 36.2 + - - +
2254A SER 4.2 8.5 - - - -
2255A HIS 3.3 27.6 + - - -
2256A TYR* 4.7 3.1 - - - -
2257A GLU* 6.0 1.6 - - - -
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Residues in contact with PRO2232 (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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2231A THR* 1.3 70.8 - - - +
2233A SER* 1.3 58.4 + - - +
2235A TYR* 3.5 9.3 - - + +
2236A GLU* 2.9 28.9 + - - +
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Residues in contact with SER2233 (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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2231A THR* 3.3 3.5 - - - -
2232A PRO* 1.3 77.2 - - - +
2234A GLY* 1.3 58.4 + - - +
2236A GLU* 3.4 5.4 + - - +
2237A TRP* 2.9 27.6 + - - +
2254A SER 6.1 0.9 - - - -
2255A HIS* 6.2 0.4 - - - -
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Residues in contact with GLY2234 (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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2193A VAL* 5.7 3.8 - - - +
2197A ALA* 5.3 0.2 - - - +
2231A THR* 3.2 10.6 + - - -
2233A SER* 1.3 76.0 - - - +
2235A TYR* 1.3 59.5 + - - +
2237A TRP* 3.7 6.4 - - - +
2238A GLY* 2.9 26.0 + - - -
2255A HIS* 3.8 34.8 - - - +
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Residues in contact with TYR2235 (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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2197A ALA* 3.7 15.0 - - + +
2230A LEU* 5.9 3.8 - - + -
2231A THR 2.7 21.4 + - - +
2232A PRO* 3.5 12.3 - - + +
2233A SER 3.2 0.2 - - - -
2234A GLY* 1.3 73.4 - - - +
2236A GLU* 1.3 57.6 + - - +
2238A GLY 3.3 0.6 + - - +
2239A ARG* 2.9 28.1 + - - +
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Residues in contact with GLU2236 (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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2232A PRO 2.9 16.7 + - - +
2233A SER* 3.8 5.2 - - - +
2235A TYR* 1.3 74.7 - - - +
2237A TRP* 1.3 60.7 + - - +
2239A ARG* 3.4 7.6 + - - +
2240A GLN* 2.9 28.2 + - - +
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Residues in contact with TRP2237 (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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2233A SER 2.9 17.4 + - - +
2234A GLY* 3.7 8.5 - - - +
2236A GLU* 1.3 79.0 - - - +
2238A GLY* 1.3 57.0 + - - +
2240A GLN* 3.2 7.4 + - - +
2241A ASN* 2.8 29.9 + - - +
2250A GLY 5.6 6.3 - - - +
2255A HIS* 5.9 2.0 - - + -
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Residues in contact with GLY2238 (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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2193A VAL* 4.5 2.9 - - - -
2194A THR* 3.8 26.2 - - - +
2197A ALA* 3.7 14.8 - - - -
2198A LYS* 5.0 1.0 + - - +
2234A GLY 2.9 16.0 + - - -
2235A TYR 3.3 1.5 + - - -
2237A TRP* 1.3 73.2 - - - +
2239A ARG* 1.3 64.5 + - - +
2241A ASN* 3.5 21.3 + - - +
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Residues in contact with ARG2239 (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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2197A ALA* 3.7 12.7 - - + +
2198A LYS* 5.3 2.9 - - - +
2201A ALA* 5.5 8.1 - - + -
2235A TYR 2.9 17.2 + - - +
2236A GLU* 3.6 9.0 - - - +
2238A GLY* 1.3 78.0 - - - +
2240A GLN* 1.3 60.1 + - - +
2241A ASN 3.5 3.8 + - - +
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Residues in contact with GLN2240 (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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2236A GLU 2.9 17.1 + - - +
2237A TRP* 3.6 8.1 - - - +
2239A ARG* 1.3 75.8 - - - +
2241A ASN* 1.3 63.6 + - - +
2242A THR* 3.5 5.2 + - - -
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Residues in contact with ASN2241 (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 5.8 0.2 - - - +
2194A THR* 4.4 15.7 - - - -
2237A TRP 2.8 16.5 + - - +
2238A GLY* 3.5 19.8 - - - +
2239A ARG 3.3 4.3 - - - +
2240A GLN* 1.3 77.5 - - - +
2242A THR* 1.3 59.0 + - - +
2243A ASP* 4.5 7.6 - - + +
2248A PRO* 6.1 4.9 - - + -
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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