Contacts of the helix formed by residues 250 - 257 (chain A) in PDB entry 6TXC
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 ILE 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.4 5.8 - - + -
134A ARG* 4.1 41.3 - - + +
135A ILE* 4.3 16.2 - - + +
244A LEU* 4.2 9.4 - - + -
245A ILE* 3.3 47.1 + - + +
248A ASN* 3.5 28.0 - - + +
249A GLY* 1.3 77.2 - - - +
251A LYS* 1.3 67.4 + - - +
252A PRO 3.3 0.7 - - - -
253A VAL* 2.9 7.8 + - + -
254A MET* 2.8 35.1 + - + -
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Residues in contact with LYS 251 (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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242A GLU* 5.0 4.4 + - - -
245A ILE* 3.8 18.1 - - + +
246A ASN* 3.8 18.6 + - - +
249A GLY* 4.5 0.2 - - - -
250A ILE* 1.3 76.8 - - - +
252A PRO* 1.4 70.0 - - + +
254A MET* 3.3 10.9 + - - +
255A GLU* 3.1 23.9 + - - +
261A PRO* 3.8 22.7 - - + +
265A ILE* 3.7 26.2 - - + -
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Residues in contact with PRO 252 (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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249A GLY* 3.6 20.6 - - - +
251A LYS* 1.4 95.0 - - + +
253A VAL* 1.3 56.8 + - + +
255A GLU* 3.4 14.8 + - - +
256A GLN* 3.0 26.2 + - - +
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Residues in contact with VAL 253 (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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130A PRO 5.6 0.2 - - - +
131A LEU* 3.8 17.3 - - + -
134A ARG* 3.4 48.9 - - + +
249A GLY 3.8 14.4 - - - +
250A ILE* 2.9 11.4 + - - +
252A PRO* 1.3 74.8 - - + +
254A MET* 1.3 66.3 + - - +
256A GLN* 3.3 19.4 + - - +
257A TYR* 3.3 39.6 - - + -
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Residues in contact with MET 254 (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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131A LEU* 4.0 16.2 - - + -
135A ILE* 6.0 0.9 - - + -
201A ILE* 4.7 5.4 - - + -
241A PHE* 5.3 0.7 - - + -
245A ILE* 4.3 7.6 - - + -
250A ILE* 2.8 34.9 + - + +
251A LYS* 3.5 12.3 - - - +
253A VAL* 1.3 76.8 - - - +
255A GLU* 1.3 61.6 + - - +
257A TYR* 3.1 9.5 + - - +
258A GLY 3.3 0.3 + - - -
259A LEU* 3.0 57.8 + - + +
261A PRO* 4.2 9.6 - - + -
264A ASP* 4.7 5.8 - - + -
265A ILE* 4.0 35.4 - - + -
268A ILE* 4.1 17.0 - - + -
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Residues in contact with GLU 255 (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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251A LYS* 3.1 13.9 + - - +
252A PRO* 3.5 14.7 - - - +
253A VAL 3.3 0.2 - - - -
254A MET* 1.3 77.9 - - - +
256A GLN* 1.3 64.6 + - - +
258A GLY* 3.0 14.4 + - - -
259A LEU 3.7 9.8 - - - +
261A PRO* 3.6 28.3 - - + +
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Residues in contact with GLN 256 (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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113A ASP* 5.9 1.8 - - - +
134A ARG* 5.8 0.3 + - - -
252A PRO 3.0 13.7 + - - +
253A VAL* 3.3 28.6 - - - +
255A GLU* 1.3 76.8 - - - +
257A TYR* 1.3 86.1 + - + +
258A GLY 3.6 1.2 + - - -
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Residues in contact with TYR 257 (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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113A ASP* 4.0 17.3 + - - +
129A HIS* 3.5 34.3 - + + +
130A PRO* 3.4 26.5 - - + +
131A LEU* 4.0 21.3 - - + -
194A ARG* 5.8 1.2 - - - +
197A LEU* 4.4 10.2 - - + +
253A VAL* 3.3 39.2 + - + -
254A MET 3.1 7.2 + - - +
256A GLN* 1.3 104.6 + - + +
258A GLY* 1.3 60.0 + - - +
259A LEU* 3.4 11.4 + - - +
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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