Contacts of the helix formed by residues 28 - 40 (chain A) in PDB entry 2CG2
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 ALA 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER* 1.3 74.5 - - - +
29A PHE* 1.3 66.2 + - + +
31A VAL* 3.4 8.7 + - - +
32A GLU* 2.9 28.9 + - - +
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Residues in contact with PHE 29 (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 SER* 3.1 6.6 + - - +
28A ALA* 1.3 82.8 - - + +
30A THR* 1.3 59.5 + - - +
32A GLU* 3.3 9.4 + - + +
33A ALA* 2.9 28.4 + - - +
460A TYR 4.8 0.7 - - - -
461A ALA 3.2 24.2 - - - -
462A ARG* 3.4 28.9 - - - -
463A GLY* 3.6 19.7 - - - +
465A TYR* 3.9 15.7 - - + +
499A GLN* 4.2 3.3 + - - +
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Residues in contact with THR 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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26A PRO* 4.0 4.5 - - + -
27A SER* 3.0 13.0 + - - -
29A PHE* 1.3 77.4 - - - +
31A VAL* 1.3 61.5 + - - +
33A ALA* 3.1 3.1 + - - +
34A GLN* 2.9 25.2 + - - +
89A ASP 3.8 14.1 - - - +
465A TYR* 3.8 0.3 - - - -
495A GLN* 2.5 33.5 + - - +
498A TYR* 3.6 30.1 - - + -
499A GLN* 3.2 30.0 + - + +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 4.1 11.4 - - + +
27A SER 2.8 26.1 + - - +
28A ALA* 3.6 8.1 - - - +
30A THR* 1.3 72.7 - - - +
32A GLU* 1.3 63.1 - - - +
34A GLN* 3.1 11.0 + - - +
35A ARG* 3.1 49.7 + - + +
89A ASP* 3.8 23.1 - - + +
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Residues in contact with GLU 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 ALA 2.9 17.7 + - - +
29A PHE* 3.3 10.3 + - + +
31A VAL* 1.3 76.9 - - - +
33A ALA* 1.3 57.9 + - - +
35A ARG* 3.3 13.1 + - - +
36A ARG* 2.7 71.5 + - + +
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Residues in contact with ALA 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 PHE 2.9 14.5 + - - +
30A THR 3.1 8.5 + - - +
32A GLU* 1.3 76.5 - - - +
34A GLN* 1.3 66.1 + - - +
36A ARG* 3.2 11.9 + - - +
37A VAL* 3.1 24.0 + - - +
499A GLN* 3.7 30.5 - - + +
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Residues in contact with GLN 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 THR* 2.9 24.6 + - - +
31A VAL 3.1 5.1 + - - +
33A ALA* 1.3 79.1 - - - +
35A ARG* 1.3 74.7 + - - +
37A VAL* 3.2 6.1 + - - +
38A GLU* 3.1 19.1 + - - +
89A ASP* 2.9 39.9 + - + +
91A ILE 3.6 16.0 - - - +
92A ASN* 3.4 20.3 + - - +
93A PRO* 3.4 21.4 - - + +
498A TYR 2.9 30.0 + - - +
499A GLN* 4.2 6.0 - - - +
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Residues in contact with ARG 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 VAL* 3.1 30.7 + - + +
32A GLU* 3.6 19.5 - - - +
33A ALA 3.3 0.4 - - - -
34A GLN* 1.3 89.9 - - - +
36A ARG* 1.3 63.6 + - - +
38A GLU* 3.3 29.3 + - - +
39A ALA* 3.0 21.3 + - - +
87A PRO* 6.0 2.0 - - - +
89A ASP* 2.7 44.2 + - - -
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Residues in contact with ARG 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 GLU* 2.7 56.4 + - + +
33A ALA* 3.2 11.0 + - - +
35A ARG* 1.3 77.3 - - - +
37A VAL* 1.3 57.1 + - + +
39A ALA* 3.0 13.0 + - - +
40A GLU* 2.9 50.9 + - - +
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Residues in contact with VAL 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 ALA 3.1 14.9 + - - +
34A GLN* 3.4 9.4 - - - +
36A ARG* 1.3 75.6 - - + +
38A GLU* 1.3 62.5 + - - +
40A GLU* 3.0 7.7 + - - +
41A LEU* 2.9 49.8 + - + +
43A PHE* 4.1 4.5 - - + -
92A ASN* 3.5 39.0 - - - +
93A PRO* 3.9 11.0 - - + -
94A SER* 3.9 5.6 - - - +
499A GLN 5.3 0.2 - - - +
501A GLU* 5.7 0.4 - - - +
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Residues in contact with GLU 38 (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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34A GLN 3.1 15.8 + - - +
35A ARG* 3.6 37.7 + - - +
37A VAL* 1.3 76.4 - - - +
39A ALA* 1.3 61.0 + - - +
40A GLU 3.5 0.2 + - - -
41A LEU 3.5 13.3 - - - +
43A PHE* 3.6 20.8 - - + +
87A PRO* 4.6 17.2 - - - +
93A PRO* 3.8 28.9 - - + +
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Residues in contact with ALA 39 (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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35A ARG 3.0 11.6 + - - +
36A ARG* 3.0 18.7 + - - +
38A GLU* 1.3 76.7 - - - +
40A GLU* 1.3 65.7 + - + +
41A LEU 4.8 0.4 - - - -
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Residues in contact with GLU 40 (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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36A ARG* 2.9 37.1 + - - +
37A VAL* 3.0 5.8 + - - +
39A ALA* 1.3 84.1 - - + +
41A LEU* 1.3 66.9 + - + +
396A ASP* 4.7 1.4 - - - +
397A GLN* 2.9 25.5 + - - +
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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