Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 1V72
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 MET 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PRO* 5.4 0.4 - - - +
39A TYR 4.2 0.7 - - - +
40A GLY* 3.2 36.3 - - - +
42A ASP* 4.3 2.0 - - - +
45A THR* 3.5 20.2 - - + +
64A LEU* 4.2 15.0 - - + +
236A ARG* 3.6 18.4 - - - +
242A LEU* 3.6 24.7 - - + -
243A SER* 3.6 26.9 - - - +
244A SER 3.1 5.3 + - - -
245A LYS* 1.3 69.4 - - - +
247A ARG* 1.3 55.9 + - - +
248A PHE 3.0 6.1 - - - -
249A LEU* 2.8 43.9 + - - +
250A SER* 2.9 17.3 + - - +
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Residues in contact with ARG 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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31A HIS* 3.2 29.7 + - + +
32A SER 4.8 3.7 + - - -
33A SER 2.9 25.4 + - - -
34A GLY 2.9 24.7 + - - -
35A GLN* 4.0 7.9 + - - +
36A ALA* 3.9 26.4 + - + +
42A ASP* 3.7 22.4 + - - +
44A LEU* 3.7 9.1 - - + +
245A LYS* 4.4 10.2 - - + +
246A MET* 1.3 76.5 - - - +
248A PHE* 1.3 82.1 + - + +
249A LEU 3.2 0.2 - - - -
250A SER* 3.7 10.5 - - - -
251A ALA* 2.7 36.7 + - - +
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Residues in contact with PHE 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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28A LEU* 3.4 26.4 - - + +
31A HIS* 3.4 29.4 - - + -
32A SER* 4.0 19.1 - - - -
245A LYS* 3.2 51.3 + - + +
246A MET 3.0 1.4 + - - -
247A ARG* 1.3 102.7 - - + +
249A LEU* 1.3 55.2 + - + +
251A ALA 4.3 0.4 - - - -
252A GLN* 2.7 36.4 + - - +
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Residues in contact with LEU 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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64A LEU* 3.9 42.4 - - + +
65A VAL* 4.1 11.7 - - - +
66A PRO* 4.4 4.7 - - + -
217A ALA 2.9 28.3 - - - +
218A ALA* 3.3 14.7 - - + +
243A SER* 3.7 25.4 - - - +
245A LYS 5.7 0.7 - - - +
246A MET* 2.8 18.4 + - - +
248A PHE* 1.3 78.7 - - + +
250A SER* 1.3 65.8 + - - +
251A ALA 3.3 0.2 - - - -
252A GLN* 3.2 10.4 + - - +
253A ILE* 3.1 26.7 + - - +
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Residues in contact with SER 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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44A LEU* 3.9 12.6 - - - -
45A THR* 2.6 43.8 + - - -
48A VAL* 3.3 7.9 - - - +
64A LEU* 3.6 17.7 - - - +
246A MET* 2.9 13.7 + - - +
247A ARG* 3.8 5.6 - - - -
249A LEU* 1.3 75.9 - - - +
251A ALA* 1.3 59.6 + - - +
253A ILE* 4.6 0.4 - - - +
254A ASP* 2.8 32.2 + - - +
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Residues in contact with ALA 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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27A ALA* 3.6 16.4 - - - +
28A LEU* 3.9 18.8 - - + -
31A HIS* 4.0 19.1 - - + -
44A LEU* 3.5 17.4 - - + +
247A ARG 2.7 24.5 + - - +
250A SER* 1.3 73.1 - - - +
252A GLN* 1.3 63.8 + - - +
254A ASP* 3.5 3.8 + - - +
255A ALA* 3.1 23.7 + - - +
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.7 25.7 - - + +
28A LEU* 4.0 14.8 - - + +
215A VAL* 3.6 13.9 - - + +
216A LEU* 3.0 20.9 + - - +
217A ALA* 2.9 47.6 + - - +
218A ALA* 3.9 3.8 - - + -
248A PHE 2.7 25.9 + - - +
249A LEU* 3.2 11.4 + - - +
251A ALA* 1.3 78.4 - - - +
253A ILE* 1.3 58.0 + - - +
255A ALA* 3.4 3.5 + - - +
256A TYR* 2.9 26.5 + - - +
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Residues in contact with ILE 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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48A VAL* 3.7 12.8 - - + -
52A PHE* 3.7 32.5 - - + -
64A LEU* 4.2 16.8 - - + -
208A PHE* 5.3 1.3 - - + -
210A ALA* 3.7 19.1 - - + -
215A VAL* 4.5 2.7 - - + -
218A ALA* 3.6 34.3 - - + +
219A GLU 4.8 3.6 - - - +
220A ALA* 5.4 2.5 - - + -
249A LEU 3.1 16.6 + - - +
250A SER* 4.0 3.1 - - - +
252A GLN* 1.3 73.5 - - - +
254A ASP* 1.3 61.3 + - - +
256A TYR* 3.2 7.6 + - + +
257A LEU* 2.8 35.5 + - + +
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA* 6.0 1.4 - - - +
31A HIS* 5.1 4.2 + - - -
44A LEU* 4.0 15.1 - - + +
47A GLN* 3.0 25.8 + - - +
48A VAL* 3.7 14.3 - - + +
51A LYS* 2.7 34.1 + - - +
250A SER 2.8 22.3 + - - +
251A ALA 3.8 4.1 - - - +
253A ILE* 1.3 73.6 - - - +
255A ALA* 1.3 58.7 + - - +
257A LEU* 3.1 12.1 + - - -
258A THR* 2.5 28.9 + - - -
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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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23A GLU* 3.8 29.3 - - + +
24A VAL* 4.0 10.5 - - + +
27A ALA* 4.0 8.7 - - + -
251A ALA 3.1 14.7 + - - +
252A GLN 3.6 4.3 - - - +
254A ASP* 1.3 79.5 + - - +
256A TYR* 1.3 64.2 + - - +
258A THR* 3.0 23.9 + - - +
261A LEU* 3.4 15.3 - - - +
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Residues in contact with TYR 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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24A VAL* 5.0 1.5 - - + +
184A ALA* 4.0 6.9 - - - +
208A PHE* 3.6 23.7 - + - -
209A GLY 3.2 16.3 + - - -
210A ALA* 3.6 27.6 - - + -
213A ASN* 3.1 41.7 + - - +
214A GLY* 5.0 0.7 - - - -
215A VAL* 3.8 20.0 - - + -
252A GLN 2.9 14.9 + - - +
253A ILE* 3.2 13.9 - - + +
255A ALA* 1.3 78.0 - - - +
257A LEU* 1.3 68.7 - - + +
258A THR 3.3 2.3 + - - -
261A LEU* 3.7 9.2 - - + +
262A TRP* 3.0 62.4 + - + +
265A ASN* 5.0 4.5 - - - -
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Residues in contact with LEU 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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48A VAL* 4.9 1.6 - - + -
51A LYS* 3.4 34.0 + - + +
52A PHE* 3.9 20.4 - - + -
55A ILE* 3.6 35.1 - - + +
208A PHE* 4.1 9.4 - - + -
253A ILE* 2.8 36.1 + - + +
254A ASP 3.3 7.0 - - - +
255A ALA 3.1 0.2 - - - -
256A TYR* 1.3 94.5 - - + +
258A THR* 1.3 55.6 + - - -
259A ASP 4.3 0.3 + - - -
260A ASP 4.9 3.3 + - - -
262A TRP* 3.8 24.7 - - + -
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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