Contacts of the helix formed by residues 247 - 257 (chain A) in PDB entry 2D7I
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 LEU 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 3.9 24.5 - - + -
149A ILE* 4.9 0.7 - - + -
172A SER* 4.2 11.0 - - - +
173A PRO* 4.4 6.3 - - + -
176A LEU* 4.1 9.9 - - + -
177A VAL* 4.1 21.1 - - + -
234A THR* 4.4 6.7 - - - +
246A TRP* 1.3 115.5 - - + +
248A PRO* 1.3 74.3 - - + +
250A LEU* 2.9 20.1 + - + +
251A LEU* 3.1 41.3 + - + +
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Residues in contact with PRO 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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74A TRP* 3.8 33.2 - - + -
140A TYR* 4.3 6.7 - - + -
144A LEU* 4.1 13.6 - - + +
171A ARG 5.8 0.4 - - - +
173A PRO* 4.3 10.5 - - + -
176A LEU* 4.1 14.4 - - + -
245A ASN* 3.4 25.6 - - - +
246A TRP 4.2 0.2 - - - +
247A LEU* 1.3 93.2 - - + +
249A PRO* 1.3 66.5 - - + +
251A LEU* 3.3 3.9 + - + +
252A ASP* 2.9 32.2 + - - +
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.4 43.6 - - + +
245A ASN* 3.7 16.6 - - - +
246A TRP 3.4 15.3 - - - +
247A LEU 3.5 2.0 - - - -
248A PRO* 1.3 99.3 - - + +
250A LEU* 1.3 58.6 + - - +
252A ASP* 4.1 1.8 - - - +
253A ARG* 3.7 17.3 + - - +
363A ILE* 3.9 24.5 - - + +
365A CYS* 4.1 7.0 - - + +
366A SER* 3.9 10.8 - - - -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A THR* 5.2 2.7 - - + -
246A TRP* 3.6 33.0 - - + +
247A LEU* 2.9 13.2 + - + +
249A PRO* 1.3 75.4 - - - +
251A LEU* 1.3 67.4 + - - +
253A ARG* 3.4 5.7 + - - +
254A ILE* 3.3 19.0 + - - +
262A VAL* 3.6 34.2 - - + +
264A PRO* 3.9 22.7 - - + -
322A PHE 6.0 0.2 - - - -
323A ALA* 4.6 14.1 - - + +
363A ILE* 3.8 17.7 - - + -
366A SER* 3.4 31.2 - - - +
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.7 12.5 - - + +
145A PRO* 3.4 29.1 - - + +
147A THR* 4.1 7.4 - - + -
176A LEU* 4.0 26.7 - - + -
232A VAL* 3.5 35.2 - - + -
234A THR* 4.8 2.0 - - - +
247A LEU* 3.1 42.6 + - + +
248A PRO 3.8 4.9 - - - +
250A LEU* 1.3 77.2 - - + +
252A ASP* 1.3 59.8 + - - +
254A ILE* 3.3 6.0 + - + +
255A ALA* 2.9 30.0 + - - +
323A ALA* 5.3 1.1 - - + -
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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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140A TYR* 3.4 30.6 - - + +
141A LEU* 3.1 30.1 + - - +
144A LEU* 3.4 12.5 - - + +
248A PRO 2.9 17.7 + - - +
249A PRO 4.3 2.0 - - - +
251A LEU* 1.3 77.1 - - - +
253A ARG* 1.3 69.0 + - - +
255A ALA* 3.0 12.4 + - - +
256A ARG* 3.1 46.7 + - - +
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Residues in contact with ARG 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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249A PRO 3.7 11.4 + - - +
250A LEU 3.4 8.9 + - - +
251A LEU 3.3 0.2 - - - -
252A ASP* 1.3 84.4 + - - +
254A ILE* 1.3 57.2 + - - +
256A ARG* 3.1 9.1 + - - +
257A ASN* 2.9 46.4 + - - +
260A THR* 4.7 2.5 - - + -
262A VAL* 3.7 20.4 - - + -
305A LYS* 6.2 1.4 - - - +
311A PRO* 3.6 39.0 + - + +
361A GLU* 2.7 40.8 + - - +
363A ILE* 4.9 2.9 - - + -
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Residues in contact with ILE 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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145A PRO* 5.6 0.9 - - + -
232A VAL* 4.3 21.5 - - + -
250A LEU 3.3 11.4 + - - +
251A LEU* 3.9 5.8 - - - +
253A ARG* 1.3 77.4 - - - +
255A ALA* 1.3 61.9 + - - +
257A ASN 3.1 20.3 - - - +
258A ARG* 3.2 14.8 + - + +
260A THR 3.5 15.3 - - - +
262A VAL* 4.1 9.4 - - + -
323A ALA* 3.6 44.4 - - + +
324A VAL* 3.7 10.3 - - - +
325A ASP* 3.9 26.2 - - + +
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Residues in contact with ALA 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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141A LEU* 4.3 14.8 - - + -
143A THR 5.5 0.2 - - - +
144A LEU* 4.3 5.2 - - + -
145A PRO* 4.0 22.9 - - + -
251A LEU 2.9 14.6 + - - +
252A ASP* 3.0 13.9 + - - +
254A ILE* 1.3 79.8 - - - +
256A ARG* 1.3 61.4 + - - +
258A ARG* 5.0 1.2 + - - +
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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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69A GLN* 4.7 7.9 - - - +
71A LEU* 4.1 19.8 - - - +
139A ARG 5.6 1.0 + - - -
140A TYR* 5.5 0.6 - - - +
141A LEU* 3.3 36.2 - - - +
252A ASP* 3.1 39.8 + - - +
253A ARG* 3.6 10.1 - - - +
255A ALA* 1.3 80.0 - - - +
257A ASN* 1.3 72.9 + - - +
258A ARG 4.1 0.6 + - - -
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Residues in contact with ASN 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 ARG* 2.9 31.8 + - - +
254A ILE* 3.1 12.2 - - - +
256A ARG* 1.3 90.5 + - - +
258A ARG* 1.3 66.6 + - - +
259A LYS 3.1 2.5 - - - +
260A THR* 3.0 35.7 + - - +
359A ARG* 5.6 7.1 - - - +
361A GLU* 5.8 1.3 - - - -
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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