Contacts of the helix formed by residues 246 - 262 (chain A) in PDB entry 2RLI
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LYS* 3.6 23.7 - - - +
245A ARG* 1.3 76.9 - - - +
247A ALA* 1.3 62.5 + - - +
248A GLU* 3.2 2.9 - - - -
249A GLN* 2.8 33.2 + - - +
250A ILE* 3.4 11.0 + - - +
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Residues in contact with ALA 247 (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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143A LYS* 4.4 14.8 - - + +
146A GLN* 5.2 6.3 - - + +
147A VAL* 3.9 24.2 - - + -
150A GLN* 4.0 14.4 - - - +
246A SER* 1.3 77.3 + - - +
248A GLU* 1.3 55.9 + - - +
250A ILE* 3.0 20.0 + - - +
251A SER* 3.0 21.4 + - - -
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Residues in contact with GLU 248 (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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150A GLN* 5.8 0.7 - - - -
246A SER 2.9 3.9 + - - +
247A ALA* 1.3 75.8 - - - +
249A GLN* 1.3 61.8 + - + +
251A SER* 4.9 2.1 - - - -
252A ASP* 3.8 18.9 + - - +
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Residues in contact with GLN 249 (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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241A TYR* 3.1 18.4 + - - +
245A ARG* 2.9 42.9 + - - +
246A SER 2.8 16.0 + - - +
248A GLU* 1.3 74.4 - - + +
250A ILE* 1.3 59.4 + - - +
251A SER 3.6 0.2 - - - -
252A ASP* 4.1 4.3 - - - +
253A SER* 3.1 23.3 + - - -
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Residues in contact with ILE 250 (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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125A LEU* 6.4 0.9 - - + -
140A GLU* 4.3 13.0 - - - +
143A LYS* 5.2 2.5 - - + +
144A LEU* 4.0 27.1 - - + -
147A VAL* 3.8 24.2 - - + -
228A ILE* 5.9 1.1 - - + -
241A TYR* 3.5 38.8 - - + +
245A ARG* 4.5 6.1 - - + -
246A SER* 3.4 26.2 - - - +
247A ALA* 3.0 8.6 + - - +
249A GLN* 1.3 73.2 - - - +
251A SER* 1.3 55.4 + - - +
253A SER* 3.0 2.4 + - - -
254A VAL* 2.7 43.1 + - + +
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Residues in contact with SER 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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147A VAL* 3.8 15.0 - - - +
150A GLN* 2.7 35.4 + - - +
151A LEU* 4.7 10.0 - - - +
154A GLU* 5.7 4.5 - - - -
157A LEU* 5.3 2.2 - - - +
247A ALA 3.0 12.7 + - - -
248A GLU* 4.9 3.1 - - - -
250A ILE* 1.3 73.8 - - - +
252A ASP* 1.3 57.2 + - - +
254A VAL* 3.5 5.2 + - - +
255A ARG* 3.0 36.8 + - - +
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Residues in contact with ASP 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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248A GLU 3.8 17.4 + - - +
249A GLN* 4.2 4.5 - - - +
250A ILE 3.3 0.6 - - - -
251A SER* 1.3 75.1 - - - +
253A SER* 1.3 58.4 + - - +
255A ARG* 3.4 14.9 + - - +
256A ARG* 2.8 71.0 + - - +
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Residues in contact with SER 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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241A TYR* 3.3 30.3 - - - -
249A GLN 3.1 20.3 + - - -
250A ILE 3.0 4.7 + - - -
252A ASP* 1.3 77.9 - - - +
254A VAL* 1.3 52.0 + - - +
256A ARG* 3.2 8.0 + - - +
257A HIS* 2.8 55.6 + - - -
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Residues in contact with VAL 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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123A TRP* 4.2 8.8 - - + -
125A LEU* 6.5 1.1 - - + -
147A VAL* 4.7 7.6 - - + -
151A LEU* 3.7 28.9 - - + -
157A LEU* 5.9 0.7 - - + -
158A PRO* 4.0 16.4 - - + -
160A VAL* 4.5 9.9 - - + -
230A LEU* 5.5 8.5 - - + -
241A TYR* 6.5 1.3 - - + -
250A ILE* 2.7 37.1 + - + +
251A SER* 3.9 6.5 - - - +
253A SER* 1.3 70.4 - - - +
255A ARG* 1.3 57.9 + - - +
257A HIS* 3.8 8.7 - - + +
258A MET* 2.9 31.1 + - - +
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 2.7 42.6 + - - +
157A LEU* 3.9 28.9 - - + +
251A SER* 3.0 21.6 + - - +
252A ASP* 3.5 19.1 - - - +
253A SER 3.3 0.2 - - - -
254A VAL* 1.3 75.5 - - - +
256A ARG* 1.3 57.2 + - + +
258A MET* 3.4 12.7 - - - +
259A ALA* 2.9 28.7 + - - +
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Residues in contact with ARG 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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252A ASP* 2.8 55.9 + - - +
253A SER* 3.2 7.4 + - - +
255A ARG* 1.3 73.6 - - + +
257A HIS* 1.3 61.6 + - - +
259A ALA* 3.1 9.3 + - + +
260A ALA* 2.9 30.2 + - - +
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Residues in contact with HIS 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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123A TRP* 3.9 13.7 - - + -
230A LEU* 5.0 13.7 - - + -
238A THR* 4.5 8.9 - - + +
239A ASP* 4.0 26.8 - - + +
240A TYR 3.1 26.9 + - - -
241A TYR* 4.6 6.8 - + + -
253A SER* 2.8 44.6 + - - +
254A VAL* 3.8 9.0 - - + +
256A ARG* 1.3 71.6 - - - +
258A MET* 1.3 57.1 + - - +
260A ALA* 3.4 6.5 + - - +
261A PHE* 2.9 33.1 + - - +
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Residues in contact with MET 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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123A TRP* 3.6 19.2 - - + -
156A GLY 3.2 26.2 - - - +
157A LEU* 4.3 12.1 - - + -
158A PRO* 3.6 24.9 - - + -
254A VAL 2.9 19.3 + - - +
255A ARG* 3.4 11.2 - - - +
257A HIS* 1.3 75.7 - - - +
259A ALA* 1.3 56.8 + - - +
262A ARG* 2.8 33.3 + - - -
263A SER* 6.1 6.7 - - - +
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Residues in contact with ALA 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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255A ARG 2.9 20.5 + - - +
256A ARG* 3.1 10.5 + - + +
258A MET* 1.3 72.6 - - - +
260A ALA* 1.3 56.6 + - - +
262A ARG* 3.3 21.1 - - - +
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Residues in contact with ALA 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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238A THR* 6.1 2.0 - - + -
256A ARG 2.9 14.7 + - - +
257A HIS* 3.7 8.1 - - - +
259A ALA* 1.3 77.0 - - - +
261A PHE* 1.3 64.4 + - - +
262A ARG* 3.5 9.2 - - - +
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Residues in contact with PHE 261 (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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123A TRP* 4.0 24.9 - + + -
232A ASN* 3.2 37.2 - - + -
233A PRO* 4.1 22.4 - - + -
236A LEU* 5.9 2.0 - - + -
237A PHE 5.0 1.1 - - - -
238A THR* 3.4 28.2 - - + +
257A HIS 2.9 16.1 + - - +
258A MET 4.3 0.2 - - - +
260A ALA* 1.3 72.9 - - - +
262A ARG* 1.3 79.1 + - - +
264A VAL* 5.6 1.2 - - - +
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Residues in contact with ARG 262 (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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258A MET* 2.8 20.8 + - - +
259A ALA* 3.3 27.4 - - - +
260A ALA 3.7 6.1 - - - +
261A PHE* 1.3 93.5 - - - +
263A SER* 1.3 66.7 + - - +
264A VAL* 3.6 26.4 - - + +
266A SER* 2.9 34.8 + - - -
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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