Contacts of the helix formed by residues 45 - 60 (chain A) in PDB entry 3CBG
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 SER 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LYS* 3.8 25.0 - - - +
4A GLY 4.2 7.0 - - - -
13A TYR* 4.9 2.2 - - - -
31A ARG* 3.3 3.6 - - - +
43A GLN 3.6 1.6 + - - -
44A ILE* 1.3 77.6 - - - +
46A PRO* 1.3 75.8 - - - +
47A GLU* 3.5 15.9 + - - +
48A GLN* 3.0 33.5 + - - +
49A ALA* 3.1 17.5 + - - +
211A GLY* 3.9 5.0 + - - -
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Residues in contact with PRO 46 (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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3A LYS 5.8 2.5 - - - +
13A TYR* 5.0 3.6 - - - +
17A GLN* 5.9 3.4 - - - +
21A ALA 5.4 6.1 - - - +
23A ASP* 3.8 18.3 - - - +
31A ARG* 3.3 20.6 - - + +
45A SER* 1.3 88.0 - - - +
47A GLU* 1.3 73.5 + - - +
49A ALA* 3.3 2.8 + - - +
50A GLN* 3.1 24.1 + - - +
73A TYR* 3.4 19.5 - - - +
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Residues in contact with GLU 47 (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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4A GLY 4.5 0.5 - - - +
5A ILE* 5.6 1.3 - - + -
13A TYR* 2.7 37.3 + - + -
16A LEU* 3.8 24.5 - - + -
17A GLN* 3.6 19.6 + - - +
20A SER* 4.3 13.0 - - - +
45A SER* 3.2 15.9 + - - +
46A PRO* 1.3 87.7 - - - +
48A GLN* 1.3 61.8 + - - +
50A GLN* 3.5 7.3 + - - +
51A PHE* 3.1 22.3 + - - +
210A LEU* 3.9 22.9 - - + +
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Residues in contact with GLN 48 (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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3A LYS* 4.0 5.3 - - - +
44A ILE* 3.4 24.9 - - + +
45A SER* 3.0 36.5 + - - +
47A GLU* 1.3 76.0 - - - +
49A ALA* 1.3 54.7 + - - +
51A PHE* 3.3 6.7 + - - +
52A LEU* 2.7 38.5 + - + +
169A ASP* 2.7 28.8 + - - +
210A LEU* 3.2 35.3 - - + +
211A GLY* 3.3 13.9 - - - -
212A ASP 4.1 1.8 - - - +
214A MET* 3.7 18.8 - - + +
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Residues in contact with ALA 49 (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 ASP* 4.4 5.2 - - - +
27A LEU* 4.8 4.3 - - + -
44A ILE* 3.7 11.1 - - + +
45A SER 3.1 5.2 + - - +
46A PRO 3.3 8.3 + - - +
48A GLN* 1.3 76.8 - - - +
50A GLN* 1.3 56.6 + - - +
52A LEU* 3.4 4.4 - - - +
53A GLY* 2.9 26.0 + - - -
73A TYR* 3.7 34.1 - - + +
77A ALA* 3.8 25.0 - - + +
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Residues in contact with GLN 50 (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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21A ALA* 3.7 36.8 + - + +
22A ASP 4.5 9.5 + - - -
23A ASP* 5.2 6.8 + - - +
24A SER 6.1 0.2 - - - +
27A LEU* 6.0 4.2 - - - +
46A PRO 3.1 15.9 + - - +
47A GLU* 3.7 7.2 - - - +
49A ALA* 1.3 77.6 - - - +
51A PHE* 1.3 57.3 + - - +
53A GLY* 3.4 2.1 + - - -
54A LEU* 3.0 38.4 + - + +
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Residues in contact with PHE 51 (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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47A GLU 3.1 18.3 + - - +
48A GLN 3.6 3.1 - - - +
50A GLN* 1.3 77.8 - - - +
52A LEU* 1.3 56.9 + - - +
54A LEU* 3.2 19.6 + - + +
55A LEU* 3.0 64.4 + - + +
58A LEU* 6.2 1.3 - - + -
208A ILE* 4.4 18.8 - - + -
210A LEU* 3.8 17.3 - - + -
214A MET* 3.9 31.4 - - + -
216A LEU* 3.9 23.8 - - + -
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Residues in contact with LEU 52 (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 ILE* 3.7 27.1 - - + -
48A GLN 2.7 15.3 + - - +
49A ALA* 3.4 6.1 - - - +
51A PHE* 1.3 74.2 - - - +
53A GLY* 1.3 62.5 + - - +
55A LEU* 3.2 13.7 + - + +
56A ILE* 3.2 25.7 + - - +
74A SER* 4.2 7.2 - - - +
77A ALA* 5.1 0.9 - - + -
78A MET* 4.0 30.9 - - + +
139A LEU* 5.5 3.8 - - + +
141A PHE* 4.2 24.2 - - + -
167A VAL* 4.2 16.2 - - + -
214A MET* 3.7 30.3 - - + -
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Residues in contact with GLY 53 (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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49A ALA 2.9 15.7 + - - -
50A GLN* 3.9 2.0 - - - -
52A LEU* 1.3 75.3 - - - +
54A LEU* 1.3 61.7 + - - +
56A ILE* 3.4 4.4 + - - -
57A SER* 3.3 19.1 + - - -
77A ALA 4.1 10.7 + - - -
81A GLN* 3.4 34.0 - - - +
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Residues in contact with LEU 54 (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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50A GLN* 3.0 25.7 + - + +
51A PHE* 3.3 23.1 - - + +
53A GLY* 1.3 78.6 - - - +
55A LEU* 1.3 56.2 + - + +
57A SER* 3.7 4.4 - - - -
58A LEU* 2.8 62.8 + - + +
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Residues in contact with LEU 55 (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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51A PHE* 3.0 62.2 + - + +
52A LEU* 3.6 15.3 - - + +
53A GLY 3.2 0.2 - - - -
54A LEU* 1.3 76.0 - - - +
56A ILE* 1.3 62.1 + - - +
58A LEU* 4.2 14.1 - - + +
59A THR* 2.9 34.6 + - - +
139A LEU* 4.5 13.2 - - + -
165A LEU* 4.4 18.4 - - + -
167A VAL* 4.6 7.6 - - + -
214A MET* 5.3 0.2 - - + -
216A LEU* 4.3 19.3 - - + -
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Residues in contact with ILE 56 (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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52A LEU 3.2 14.7 + - - +
53A GLY 3.4 8.0 + - - +
55A LEU* 1.3 74.6 - - - +
57A SER* 1.3 58.5 + - - +
59A THR* 4.6 0.2 - - - -
60A GLY* 3.1 22.9 + - - -
61A ALA* 3.3 19.3 + - + +
64A VAL* 3.7 28.5 - - + -
78A MET* 3.8 34.1 - - + +
81A GLN* 3.6 30.5 - - + +
82A LEU* 4.0 17.0 - - + +
139A LEU* 4.2 17.3 - - + -
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Residues in contact with SER 57 (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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53A GLY 3.3 10.1 + - - -
54A LEU* 3.7 10.3 - - - -
55A LEU 3.2 0.2 - - - -
56A ILE* 1.3 79.2 - - - +
58A LEU* 1.3 75.0 + - - +
60A GLY* 3.1 14.3 + - - -
81A GLN* 4.9 16.4 - - - -
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Residues in contact with LEU 58 (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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51A PHE* 6.2 1.3 - - + -
54A LEU* 2.8 64.0 + - + +
55A LEU* 4.2 15.5 - - + +
57A SER* 1.3 81.2 - - - +
59A THR* 1.3 59.8 + - - +
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Residues in contact with THR 59 (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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55A LEU* 2.9 20.2 + - - +
58A LEU* 1.3 79.3 - - - +
60A GLY* 1.3 57.4 + - - +
61A ALA* 3.0 35.7 - - + +
138A ASP* 5.0 6.5 - - + +
139A LEU* 5.0 9.2 - - + -
161A ARG* 4.5 17.6 + - - +
163A GLY 5.6 1.9 + - - -
165A LEU* 4.9 15.3 - - + +
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Residues in contact with GLY 60 (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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56A ILE 3.1 9.1 + - - -
57A SER 3.1 9.7 + - - -
58A LEU 3.5 0.4 + - - -
59A THR* 1.3 76.4 - - - +
61A ALA* 1.3 66.8 + - - +
62A LYS* 3.5 17.2 - - - +
83A PRO* 4.7 4.6 - - - +
138A ASP* 4.8 1.1 - - - +
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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