Contacts of the helix formed by residues 55 - 68 (chain A) in PDB entry 2CMG
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 LEU 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.3 10.5 - - + -
51A PHE 3.2 27.1 + - - +
52A LYS* 3.8 11.3 + - - +
53A ASN 3.8 0.8 - - - -
54A PHE* 1.3 77.6 - - - +
56A HIS* 1.3 55.5 + - - +
57A ILE 3.0 1.4 + - - -
58A GLU* 3.7 3.5 + - - +
59A SER* 2.7 31.7 + - - -
83A ASP* 6.1 0.2 - - - +
85A GLU* 3.9 13.0 - - + +
113A PHE* 3.8 26.0 - - + +
114A PHE* 3.4 37.2 - - + -
115A PRO* 3.8 22.4 - - + -
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Residues in contact with HIS 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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53A ASN 3.8 19.3 + - - -
54A PHE* 3.0 16.2 + + + -
55A LEU* 1.3 78.6 + - - +
57A ILE* 1.3 67.4 + - + +
59A SER* 3.3 7.9 - - - -
60A GLU* 3.0 49.8 + - + +
89A GLN* 5.0 5.8 - - - +
235A ARG* 3.0 61.7 + - + +
236A TYR* 4.0 21.3 - - + +
251B ASN* 5.2 6.7 + - - -
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Residues in contact with ILE 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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54A PHE* 2.9 49.2 + - + +
55A LEU 3.0 0.6 - - - -
56A HIS* 1.3 96.0 - - + +
58A GLU* 1.3 62.5 + - - +
61A LEU* 3.1 20.1 + - - +
200A ALA* 4.9 1.6 - - + -
203A ARG* 3.2 49.6 - - + +
236A TYR* 3.8 35.0 - - + -
175B LEU* 4.5 15.5 - - + -
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Residues in contact with GLU 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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50A LEU* 5.6 5.7 - - - +
54A PHE 4.4 0.4 + - - -
55A LEU* 3.7 4.0 + - - +
57A ILE* 1.3 79.4 - - - +
59A SER* 1.3 61.7 + - - +
61A LEU* 3.2 5.0 + - + -
62A LEU* 2.9 52.4 + - + +
83A ASP* 4.7 10.2 - - - +
200A ALA* 6.0 1.3 - - - -
203A ARG* 4.6 16.1 - - - +
208A LYS* 2.8 33.6 + - - +
210A TYR* 2.6 32.7 + - + +
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Residues in contact with SER 59 (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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55A LEU 2.7 25.2 + - - -
56A HIS* 3.3 9.7 - - - -
58A GLU* 1.3 77.8 - - - +
60A GLU* 1.3 61.6 + - - +
62A LEU* 5.1 0.2 - - - -
63A ALA* 3.0 30.8 + - - +
83A ASP* 4.5 7.1 + - - -
85A GLU* 3.7 39.9 + - - +
86A LEU* 3.7 9.5 - - - +
89A GLN* 3.5 11.1 + - - +
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Residues in contact with GLU 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 HIS* 3.0 38.2 + - - +
57A ILE 3.9 1.8 - - - +
59A SER* 1.3 78.1 + - - +
61A LEU* 1.3 63.9 + - - +
64A HIS* 3.0 38.7 + - + +
89A GLN* 3.6 27.1 + - - +
233A SER 4.7 1.0 - - - +
234A VAL* 3.5 11.3 - - - +
235A ARG* 2.7 28.6 + - - +
236A TYR* 2.6 27.8 + - + -
237A TYR* 2.7 29.3 + - + +
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Residues in contact with LEU 61 (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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57A ILE 3.1 18.1 + - - +
58A GLU* 3.8 6.1 - - + +
60A GLU* 1.3 76.7 - - - +
62A LEU* 1.3 64.9 + - + +
65A MET* 3.0 43.8 + - + +
198A PHE* 3.3 37.5 - - + -
199A VAL 4.7 8.1 - - - +
200A ALA* 4.9 7.2 - - + -
201A PRO* 5.1 0.4 - - + -
210A TYR* 5.2 4.7 - - + -
236A TYR* 4.1 12.1 - - + +
237A TYR* 4.2 16.4 - - + +
241A ILE* 4.0 27.1 - - + +
242A HIS* 5.0 0.7 - - - -
245A ALA* 4.9 7.4 - - + -
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Residues in contact with LEU 62 (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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58A GLU* 2.9 47.4 + - + +
61A LEU* 1.3 73.6 - - + +
63A ALA* 1.3 64.0 + - - +
65A MET* 3.4 14.4 + - - +
66A GLY 3.8 1.6 + - - -
83A ASP* 4.9 3.8 - - - +
86A LEU* 3.8 23.3 - - + -
144A PHE* 3.1 26.8 - - + -
146A LEU* 4.7 11.9 - - + -
168A ILE* 4.0 10.5 - - + -
170A VAL* 5.4 4.3 - - + -
198A PHE* 4.0 20.6 - - + -
210A TYR* 3.6 31.0 - - + -
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Residues in contact with ALA 63 (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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59A SER 3.0 20.3 + - - +
60A GLU 4.1 0.2 - - - +
62A LEU* 1.3 82.1 - - - +
64A HIS* 1.3 60.3 + - + +
67A GLY* 3.2 20.6 + - - -
86A LEU* 3.3 22.4 - - + +
89A GLN* 3.5 23.6 - - + -
90A LEU* 3.6 23.9 - - + +
93A TYR* 4.0 1.7 - - - -
144A PHE* 4.1 1.9 - - - -
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Residues in contact with HIS 64 (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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60A GLU* 3.0 23.7 + - - +
61A LEU 4.1 0.2 - - - -
63A ALA* 1.3 76.4 - - - +
65A MET* 1.3 63.7 + - - +
66A GLY 3.3 1.1 - - - -
67A GLY 3.6 1.6 - - - -
68A CYS* 3.0 16.1 + - - +
89A GLN* 3.0 51.3 + - + +
92A LYS* 4.2 5.5 - - - +
93A TYR* 3.0 39.0 - + - +
231A LEU* 3.6 15.3 - - + +
234A VAL* 3.4 20.6 - - + +
237A TYR* 3.3 42.9 + - + -
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Residues in contact with MET 65 (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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61A LEU* 3.0 49.0 + - + +
62A LEU* 3.6 8.3 - - - +
63A ALA 3.3 0.4 - - - -
64A HIS* 1.3 79.8 - - - +
66A GLY* 1.3 51.8 + - - +
69A THR* 2.7 29.5 + - - +
168A ILE* 4.2 9.6 - - + -
198A PHE* 4.1 17.3 - - + -
212A TYR* 3.6 22.9 - - + -
219A PRO* 4.4 0.2 - - - -
237A TYR* 4.7 0.7 - - - -
242A HIS* 3.3 50.7 - - - +
245A ALA* 4.5 2.2 - - + -
246A PHE* 3.6 36.6 - - + -
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Residues in contact with GLY 66 (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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62A LEU 3.8 6.2 + - - -
65A MET* 1.3 78.4 - - - +
67A GLY* 1.3 66.5 + - - +
68A CYS 3.3 0.7 - - - -
69A THR* 3.0 22.8 + - - +
70A LYS* 3.7 13.5 + - - +
73A LEU* 5.1 0.3 - - - +
142A LEU* 4.0 29.6 - - - +
144A PHE* 5.4 0.2 - - - -
166A VAL* 5.1 0.8 - - - +
168A ILE* 4.3 9.6 - - - +
212A TYR* 4.4 0.4 - - - -
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Residues in contact with GLY 67 (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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63A ALA 3.2 13.6 + - - -
64A HIS 3.6 0.2 + - - -
65A MET 3.4 0.2 - - - -
66A GLY* 1.3 78.3 - - - +
68A CYS* 1.3 57.6 + - - +
69A THR 3.7 0.2 + - - -
70A LYS 3.7 14.7 - - - +
73A LEU* 3.8 17.4 - - - +
93A TYR* 3.5 37.7 - - - -
142A LEU* 4.2 1.8 - - - +
227A LYS* 3.7 5.9 - - - +
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Residues in contact with CYS 68 (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 HIS 3.0 17.4 + - - +
65A MET 4.6 0.2 - - - -
67A GLY* 1.3 75.0 - - - +
69A THR* 1.3 57.2 + - - +
70A LYS 3.4 4.0 - - - -
93A TYR* 3.4 17.5 - - - -
223A LEU* 3.6 5.8 - - + +
224A MET* 2.9 36.8 + - - +
227A LYS* 3.7 15.7 - - - -
228A ILE* 3.5 49.4 - - + -
231A LEU* 4.3 2.7 - - - -
237A TYR* 3.7 12.3 - - - +
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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