Contacts of the helix formed by residues 27 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 2.8 53.6 + - + +
26A ASP* 1.3 80.7 - - + +
28A MSE 1.3 65.4 + - - +
29A HIS 3.5 1.1 - - - -
30A PRO* 3.3 10.3 - - - +
31A PHE* 3.2 46.2 + - + -
199A PHE* 3.9 11.7 - - + -
212A LEU* 4.4 15.5 - - + -
222A LEU* 4.0 22.0 - - + -
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Residues in contact with MSE 28 (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 PHE* 3.0 44.4 + - + +
24A ASP* 3.2 20.6 - - + +
27A VAL* 1.3 76.4 - - - +
29A HIS* 1.3 58.9 + - - +
31A PHE* 3.1 4.0 + - - +
32A MSE 2.8 50.2 + - + +
110A HIS* 5.6 2.7 - - + -
198A ILE* 3.6 32.3 - - + +
199A PHE* 3.6 26.2 - - - -
237A ALA* 3.6 13.9 - - + -
238A SER* 3.7 20.2 - - - +
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Residues in contact with HIS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.0 24.7 + - + +
25A PHE* 3.4 44.3 + + - +
28A MSE 1.3 73.8 - - - +
30A PRO* 1.3 71.1 - - + +
32A MSE 3.1 19.8 + - + +
33A VAL* 3.1 19.4 + - - +
54A ASP* 4.2 8.3 + - + +
55A PHE* 3.6 50.1 + + + -
58A ARG* 3.6 15.3 + - - +
251A TRS 3.6 23.0 + - - -
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Residues in contact with PRO 30 (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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25A PHE 3.6 13.0 - - - +
26A ASP 3.3 18.2 - - - +
27A VAL* 3.3 14.4 - - - +
29A HIS* 1.3 94.1 - - + +
31A PHE* 1.3 63.8 + - + +
33A VAL* 3.4 6.9 + - + +
34A ARG* 3.1 23.7 + - - +
58A ARG* 3.7 26.9 - - - +
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Residues in contact with PHE 31 (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 VAL* 3.2 36.7 + - + -
28A MSE 3.1 9.1 + - - +
30A PRO* 1.3 76.7 - - + +
32A MSE 1.3 60.6 + - - +
34A ARG* 3.6 20.6 - - - +
35A ALA* 2.9 29.8 + - - +
198A ILE* 3.8 17.7 - - + -
199A PHE* 3.7 28.3 - + + -
222A LEU* 3.5 25.8 - - + -
223A ASP* 3.5 23.6 - - - -
226A TYR* 3.5 33.1 - + + -
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Residues in contact with MSE 32 (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 MSE 2.8 34.7 + - + +
29A HIS* 3.1 26.7 + - + +
31A PHE* 1.3 77.7 - - - +
33A VAL* 1.3 61.4 + - - +
35A ALA* 3.3 1.7 + - - +
36A PHE* 3.1 36.3 + - + -
55A PHE* 3.9 15.7 - - + -
109A THR* 4.3 20.0 - - - -
110A HIS* 3.3 41.5 - - + +
139A VAL* 4.1 6.1 - - + -
198A ILE* 3.8 27.1 - - + -
238A SER* 4.0 7.2 - - - +
251A TRS 5.1 1.6 - - - +
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Residues in contact with VAL 33 (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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29A HIS 3.1 13.1 + - - +
30A PRO* 3.7 7.9 - - + +
31A PHE 3.3 0.2 - - - -
32A MSE 1.3 73.5 - - - +
34A ARG* 1.3 60.9 + - - +
36A PHE* 3.2 7.3 + - - +
37A THR* 2.6 35.2 + - - +
40A PHE* 4.8 5.8 - - + -
55A PHE* 3.7 21.3 - - + -
58A ARG* 3.9 24.7 - - + +
59A LEU* 4.4 8.7 - - + -
62A HIS* 3.3 35.4 - - + +
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Residues in contact with ARG 34 (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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30A PRO 3.1 14.0 + - - +
31A PHE* 3.6 26.8 - - - +
32A MSE 3.3 0.2 - - - -
33A VAL* 1.3 76.2 - - - +
35A ALA* 1.3 63.7 + - - +
37A THR* 3.4 7.2 + - - -
38A PRO* 3.3 19.1 - - - +
223A ASP* 3.1 34.2 + - - +
226A TYR* 3.5 38.6 + - + +
227A GLN* 4.4 15.4 - - - +
192B VAL 5.1 8.3 + - - -
193B THR* 5.5 2.3 - - - +
195B ARG* 5.2 1.6 - - - +
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Residues in contact with ALA 35 (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 PHE 2.9 17.3 + - - +
32A MSE 3.6 4.9 - - - +
33A VAL 3.2 0.2 - - - -
34A ARG* 1.3 77.7 - - - +
36A PHE* 1.3 60.5 + - + +
38A PRO* 3.7 5.3 - - - +
39A PHE* 3.5 20.1 - - - -
197A GLY 5.7 0.7 - - - +
198A ILE* 3.9 27.4 - - + -
226A TYR* 3.3 17.0 + - + +
230A GLN* 5.2 3.6 - - - +
240A PHE* 3.6 13.7 - - + -
194B TYR* 5.4 4.4 - - + -
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Residues in contact with PHE 36 (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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32A MSE 3.1 27.9 + - + +
33A VAL* 3.2 3.8 + - - +
35A ALA* 1.3 79.6 - - - +
37A THR* 1.3 67.4 + - - +
38A PRO* 3.3 0.7 - - - -
39A PHE* 2.8 18.1 + - - +
40A PHE* 3.2 33.8 + + + -
55A PHE* 3.9 27.6 - + - -
59A LEU* 5.0 0.9 - - + -
107A VAL* 4.3 6.3 - - + -
109A THR* 3.6 16.4 - - + -
137A PHE* 3.4 37.0 - + + -
139A VAL* 3.5 33.9 - - + -
198A ILE* 4.5 3.4 - - + -
240A PHE* 3.7 20.9 - + - -
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Residues in contact with THR 37 (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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33A VAL* 2.6 23.5 + - - +
34A ARG* 3.7 6.9 - - - -
35A ALA 3.4 0.2 - - - -
36A PHE* 1.3 76.9 - - - +
38A PRO* 1.3 72.2 - - + +
39A PHE 3.0 1.4 + - - -
40A PHE* 3.2 26.2 + - + +
62A HIS* 3.7 29.4 + - + +
135B ARG* 4.5 5.0 + - - +
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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