Contacts of the helix formed by residues 27 - 37 (chain B) in PDB entry 2P7I
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 VAL 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B PHE* 2.9 47.2 + - + +
26B ASP* 1.3 85.1 - - + +
28B MSE 1.3 64.9 + - - +
29B HIS 3.5 0.4 - - - -
30B PRO* 3.3 12.0 - - - +
31B PHE* 3.2 31.0 + - + -
199B PHE* 3.8 23.8 - - + -
212B LEU* 4.1 19.7 - - + -
222B LEU* 4.1 21.8 - - + -
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Residues in contact with MSE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 2.9 44.6 + - + +
24B ASP* 3.4 18.8 - - + +
27B VAL* 1.3 75.2 - - - +
29B HIS* 1.3 60.7 + - + +
31B PHE* 3.3 3.4 + - - +
32B MSE 2.9 49.9 + - + +
110B HIS* 5.5 2.5 - - + -
198B ILE* 3.6 34.8 - - + +
199B PHE* 3.6 27.4 - - - -
237B ALA* 3.8 9.2 - - + -
238B SER* 3.7 23.3 - - - +
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 3.0 27.1 + - + +
25B PHE* 3.5 44.7 + + - +
28B MSE 1.3 75.4 - - + +
30B PRO* 1.3 70.4 - - + +
32B MSE 3.2 17.1 + - + +
33B VAL* 3.1 19.8 + - - +
54B ASP* 4.2 18.6 + - + +
55B PHE* 3.6 39.1 + + + -
58B ARG* 3.7 16.0 + - - +
251B TRS 4.1 19.5 + - - -
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PHE 3.6 12.6 - - - +
26B ASP 3.2 20.2 - - - +
27B VAL* 3.3 13.5 - - - +
29B HIS* 1.3 95.0 - - + +
31B PHE* 1.3 58.0 + - + +
33B VAL* 3.3 6.2 + - + +
34B ARG* 3.0 28.2 + - - +
58B ARG* 3.7 29.1 - - - +
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.2 30.6 + - + +
28B MSE 3.3 3.7 + - - +
30B PRO* 1.3 75.6 - - + +
32B MSE 1.3 60.7 + - - +
34B ARG* 3.3 21.8 + - - +
35B ALA* 2.8 29.6 + - - +
198B ILE* 3.9 13.0 - - + -
199B PHE* 3.7 35.4 - + + -
222B LEU* 3.6 24.2 - - + -
223B ASP* 3.4 26.2 - - - -
226B TYR* 3.5 37.7 - + + -
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Residues in contact with MSE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MSE 2.9 35.8 + - + +
29B HIS* 3.2 18.1 + - + +
31B PHE* 1.3 77.0 - - - +
33B VAL* 1.3 57.8 + - - +
35B ALA* 3.2 1.6 + - - +
36B PHE* 3.0 42.3 + - + -
55B PHE* 4.0 21.8 - - + -
109B THR* 4.4 17.7 - - - -
110B HIS* 3.3 41.3 - - + +
139B VAL* 4.0 8.5 - - + -
198B ILE* 4.0 25.5 - - + +
238B SER* 3.9 8.3 - - - +
251B TRS 6.1 1.1 - - - -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS 3.1 13.0 + - - +
30B PRO* 3.7 8.5 - - + +
32B MSE 1.3 76.5 - - - +
34B ARG* 1.3 57.3 + - - +
36B PHE* 3.2 8.1 + - - +
37B THR* 2.7 33.6 + - - +
40B PHE* 5.0 5.6 - - + -
55B PHE* 3.7 22.4 - - + -
58B ARG* 3.9 26.5 - - + +
59B LEU* 4.5 8.3 - - + -
62B HIS* 3.5 34.1 - - + +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLN* 4.4 17.0 - - - +
192A VAL 5.2 3.2 + - - -
193A THR* 5.8 1.2 - - - +
194A TYR* 4.8 0.2 - - - -
195A ARG* 5.5 1.0 - - - +
30B PRO 3.0 14.8 + - - +
31B PHE* 3.5 29.0 - - - +
32B MSE 3.3 0.2 - - - -
33B VAL* 1.3 78.9 - - - +
35B ALA* 1.3 60.7 + - - +
36B PHE 3.3 0.2 + - - -
37B THR* 3.3 13.4 + - - -
38B PRO* 3.4 11.6 - - - +
219B LYS* 5.7 0.6 - - - +
223B ASP* 3.1 34.1 + - - +
226B TYR* 3.6 38.3 + - + +
227B GLN* 4.6 12.7 - - - +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A TYR* 2.9 35.8 + - - +
31B PHE 2.8 20.0 + - - +
32B MSE 3.4 5.6 - - - +
34B ARG* 1.3 73.9 - - - +
36B PHE* 1.3 61.1 + - + +
38B PRO* 3.6 0.9 - - - +
39B PHE* 3.6 9.0 - - - -
197B GLY 5.8 0.2 - - - +
198B ILE* 3.8 29.6 - - + -
226B TYR* 3.4 16.5 + - + +
240B PHE* 3.7 5.2 - - + -
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B MSE 3.0 28.7 + - + +
33B VAL* 3.7 3.8 - - - +
35B ALA* 1.3 79.2 - - + +
37B THR* 1.3 62.8 + - - +
38B PRO 3.4 0.2 - - - -
39B PHE* 2.9 19.5 + - - +
40B PHE* 3.3 35.4 + + + -
55B PHE* 3.9 22.7 - + - -
59B LEU* 4.9 1.1 - - + -
107B VAL* 4.2 8.7 - - + -
109B THR* 3.3 34.1 - - + -
137B PHE* 3.6 37.3 - + + -
139B VAL* 3.5 22.0 - - + -
198B ILE* 4.5 4.3 - - + -
240B PHE* 3.8 19.5 - + - -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 4.6 3.9 + - - +
33B VAL* 2.7 23.9 + - - +
34B ARG* 3.7 6.9 - - - -
36B PHE* 1.3 76.6 - - - +
38B PRO* 1.3 70.4 - - + +
39B PHE 3.1 1.0 + - - -
40B PHE* 3.4 25.2 + - + +
62B HIS* 3.6 29.2 + - + +
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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