Contacts of the helix formed by residues 251 - 260 (chain A) in PDB entry 5IJ0
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 ASP 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG* 5.9 0.2 + - - -
133A GLN* 2.6 40.4 + - - +
242A LEU* 4.2 8.9 - - + +
249A ASN 4.2 0.2 - - - -
250A VAL* 1.3 79.2 - - - +
252A LEU* 1.3 65.0 + - - +
253A THR* 2.7 39.9 + - - +
254A GLU* 3.0 43.6 + - + +
255A PHE* 3.4 5.4 + - - -
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Residues in contact with LEU 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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4A CYS* 4.8 20.0 - - + -
133A GLN* 4.6 13.7 - - + +
134A GLY* 5.2 3.1 - - - -
135A PHE 5.3 0.9 - - - +
136A LEU* 5.1 5.8 - - + -
165A SER* 4.0 21.1 - - - +
167A LEU* 3.7 30.3 - - + +
238A ILE* 4.4 11.9 - - + -
239A THR* 6.3 2.2 - - + -
242A LEU* 3.7 24.6 - - + +
250A VAL 4.0 0.2 + - - -
251A ASP* 1.3 77.8 + - - +
253A THR* 1.3 57.5 - - - +
255A PHE* 3.0 28.8 + - + +
256A GLN* 2.9 30.3 + - - +
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Residues in contact with THR 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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133A GLN* 5.6 2.3 + - - +
165A SER* 5.0 6.8 + - - -
251A ASP* 2.7 27.4 + - - -
252A LEU* 1.3 72.8 - - - +
254A GLU* 1.3 50.4 + - + +
256A GLN* 3.3 19.3 + - + +
257A THR* 2.7 46.0 + - - +
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Residues in contact with GLU 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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249A ASN 3.7 12.1 - - - +
250A VAL* 3.5 21.1 - - + +
251A ASP* 3.0 36.7 + - + +
253A THR* 1.3 77.0 - - - +
255A PHE* 1.3 61.1 + - - +
257A THR* 4.1 5.2 - - - -
258A ASN* 2.6 47.4 + - - +
352A LYS* 3.8 13.6 + - - -
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Residues in contact with PHE 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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167A LEU* 5.5 7.2 - - + -
200A CYS* 6.5 0.7 - - - -
202A PHE* 6.1 6.1 - + + -
238A ILE* 3.6 22.9 - - + -
241A SER* 4.0 8.1 - - - -
242A LEU* 6.0 0.4 - - + -
250A VAL* 3.4 30.7 - - + -
251A ASP 3.4 2.6 + - - -
252A LEU* 3.0 35.7 + - + +
254A GLU* 1.3 74.9 - - - +
256A GLN* 1.3 59.9 + - + +
258A ASN* 5.0 0.7 - - - -
259A LEU* 2.8 56.0 + - + +
316A CYS* 3.5 32.5 - - + -
318A LEU* 3.6 26.7 - - + -
352A LYS* 5.2 2.2 - - + -
378A LEU* 4.7 7.0 - - + -
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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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163A LYS 5.2 3.8 - - - +
165A SER* 2.6 44.5 + - - +
166A LYS 3.6 1.0 - - - +
167A LEU* 4.4 11.2 - - + +
199A ASP* 3.3 32.5 + - + +
200A CYS* 5.4 4.7 - - + -
252A LEU 2.9 14.7 + - - +
253A THR* 3.4 19.2 + - + +
255A PHE* 1.3 77.3 - - - +
257A THR* 1.3 61.7 + - - +
260A VAL* 3.3 33.5 - - + +
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Residues in contact with THR 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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253A THR* 2.7 35.4 + - - +
254A GLU* 3.5 9.3 - - - -
255A PHE 3.2 0.2 - - - -
256A GLN* 1.3 76.8 - - - +
258A ASN* 1.3 69.8 + - - +
260A VAL 3.7 11.8 - - - +
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Residues in contact with ASN 258 (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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254A GLU* 2.6 43.3 + - - +
255A PHE* 4.4 1.1 - - + +
257A THR* 1.3 81.5 - - - +
259A LEU* 1.3 69.8 + - + +
260A VAL 3.5 3.1 + - - -
261A PRO* 4.9 0.3 - - - +
314A ALA* 3.6 13.8 - - - +
316A CYS* 6.1 0.2 - - + -
352A LYS* 3.6 40.7 - - + +
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Residues in contact with LEU 259 (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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200A CYS* 5.5 4.5 - - - -
202A PHE* 5.2 2.5 - - + -
255A PHE* 2.8 36.7 + - + +
258A ASN* 1.3 77.6 - - + +
260A VAL* 1.3 63.4 + - + +
261A PRO* 3.2 7.7 - - - +
265A ILE 5.0 0.3 - - - +
266A HIS* 5.7 0.2 - - - -
268A PRO* 4.6 15.7 - - + -
314A ALA* 3.8 17.9 - - + +
315A CYS 4.4 0.7 - - - -
316A CYS* 3.6 36.1 - - + +
352A LYS* 6.1 0.2 - - + -
378A LEU* 3.8 40.2 - - + +
380A ASN* 2.6 33.9 + - - +
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Residues in contact with VAL 260 (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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199A ASP 4.2 9.4 - - - +
200A CYS* 5.2 5.6 - - + -
256A GLN* 3.3 27.8 + - + +
257A THR 3.7 12.7 - - - +
258A ASN 3.3 2.4 - - - -
259A LEU* 1.3 83.6 - - + +
261A PRO* 1.3 60.9 - - - +
262A TYR 2.9 33.2 - - - +
263A PRO* 4.3 6.7 - - + +
265A ILE 3.7 7.0 - - - +
266A HIS* 4.1 21.8 - - + +
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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