Contacts of the helix formed by residues 55 - 68 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B LEU* 4.4 10.8 - - + -
51B PHE 3.1 18.3 + - - +
52B LYS* 3.0 24.3 + - - +
53B ASN 3.7 0.2 - - - -
54B PHE* 1.3 77.7 - - - +
56B HIS* 1.3 61.1 + - - +
57B ILE* 3.3 3.0 + - - +
58B GLU* 4.0 2.6 + - - +
59B SER* 2.9 25.1 + - - -
83B ASP* 6.1 0.4 - - - +
85B GLU* 4.2 14.3 - - + +
113B PHE* 3.6 43.3 - - + +
114B PHE* 4.0 21.1 - - + -
115B PRO* 3.6 17.7 - - + -
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Residues in contact with HIS 56 (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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251A ASN* 4.6 18.3 + - - -
53B ASN 3.5 26.3 + - - -
54B PHE* 3.7 15.3 - + - -
55B LEU* 1.3 78.3 - - - +
57B ILE* 1.3 87.4 + - + +
59B SER* 3.3 7.0 - - - -
60B GLU* 2.9 50.4 + - + +
85B GLU* 5.7 2.0 + - - -
89B GLN* 5.4 3.1 - - - +
235B ARG* 4.4 24.5 - - + +
236B TYR* 4.0 11.9 - + + +
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Residues in contact with ILE 57 (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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175A LEU* 5.6 7.6 - - + -
54B PHE* 2.6 38.3 + - + +
55B LEU* 4.7 1.8 - - - +
56B HIS* 1.3 90.4 - - + +
58B GLU* 1.3 87.4 + - + +
61B LEU* 3.0 26.0 + - - +
200B ALA* 5.8 2.5 - - + -
203B ARG* 2.9 47.8 - - + +
236B TYR* 3.5 43.6 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 5.9 2.9 - - - +
55B LEU 4.0 2.0 + - - +
57B ILE* 1.3 96.1 - - + +
59B SER* 1.3 63.1 + - - +
61B LEU* 4.4 5.8 - - + -
62B LEU* 3.1 53.2 + - + +
83B ASP* 4.6 13.0 - - - +
146B LEU* 5.9 1.7 - - - +
200B ALA* 5.7 2.7 - - - -
203B ARG* 5.0 7.6 + - - +
208B LYS* 2.5 35.7 + - - +
210B TYR* 3.0 25.5 + - + +
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Residues in contact with SER 59 (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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55B LEU 2.9 24.3 + - - -
56B HIS* 3.1 11.1 + - - -
58B GLU* 1.3 78.5 - - - +
60B GLU* 1.3 60.4 + - - +
63B ALA* 3.1 29.8 + - - +
83B ASP* 4.7 7.4 + - - -
85B GLU* 3.6 38.8 + - - +
86B LEU* 3.7 12.4 - - - +
89B GLN* 3.7 11.7 + - - +
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Residues in contact with GLU 60 (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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56B HIS* 2.9 42.5 + - - +
57B ILE 3.7 2.0 - - - +
59B SER* 1.3 75.4 + - - +
61B LEU* 1.3 65.1 + - - +
64B HIS* 2.9 41.2 + - + +
89B GLN* 3.3 27.0 + - + +
234B VAL* 3.1 28.4 - - - +
235B ARG* 3.1 24.9 + - - -
236B TYR* 3.1 8.3 + - + -
237B TYR* 3.1 23.6 + - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE 3.0 17.9 + - - +
58B GLU* 3.9 4.5 - - - +
60B GLU* 1.3 75.8 - - - +
62B LEU* 1.3 62.9 + - + +
64B HIS 3.9 0.2 - - - -
65B MET* 2.9 50.9 + - + +
198B PHE* 3.6 30.7 - - + -
199B VAL 4.2 9.2 - - - +
200B ALA* 4.2 15.7 - - + -
210B TYR* 4.4 3.6 - - + -
236B TYR* 4.0 18.8 - - + +
237B TYR* 4.2 22.0 - - + -
241B ILE* 4.4 11.7 - - + -
242B HIS* 5.2 1.3 - - - -
245B ALA* 4.8 5.2 - - + -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.1 40.6 + - + +
61B LEU* 1.3 76.9 - - + +
63B ALA* 1.3 69.8 + - - +
65B MET* 3.4 12.0 + - - +
66B GLY 3.5 5.2 + - - -
83B ASP* 5.3 2.5 - - - +
86B LEU* 4.2 7.9 - - + -
144B PHE* 3.2 31.0 - - + -
146B LEU* 5.0 16.8 - - + -
168B ILE* 3.7 11.6 - - + +
170B VAL* 5.7 4.3 - - + -
198B PHE* 3.8 32.3 - - + -
210B TYR* 4.0 22.7 - - + -
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Residues in contact with ALA 63 (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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59B SER 3.1 21.4 + - - +
60B GLU 3.8 1.8 - - - +
62B LEU* 1.3 81.8 - - - +
64B HIS* 1.3 62.7 + - - +
66B GLY* 3.3 1.0 + - - -
67B GLY* 2.9 22.5 + - - -
86B LEU* 3.6 14.9 - - + +
89B GLN* 3.5 26.2 - - + -
90B LEU* 4.0 25.1 - - + +
93B TYR* 4.1 1.1 - - + -
144B PHE* 4.2 0.9 - - - -
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Residues in contact with HIS 64 (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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60B GLU* 2.9 30.9 + - + +
63B ALA* 1.3 71.7 - - + +
65B MET* 1.3 64.2 + - - +
66B GLY 3.1 1.8 - - - -
67B GLY 3.7 0.7 - - - -
68B CYS* 2.9 26.6 + - - +
89B GLN* 2.8 50.6 + - + -
92B LYS* 4.2 3.1 - - + -
93B TYR* 2.8 27.8 + + - +
231B LEU* 3.3 31.5 - - + +
234B VAL* 3.5 7.9 - - + +
237B TYR* 3.5 39.1 + - + -
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Residues in contact with MET 65 (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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61B LEU* 2.9 43.1 + - + +
62B LEU* 3.6 9.4 - - - +
63B ALA 3.3 0.2 - - - -
64B HIS* 1.3 78.2 - - - +
66B GLY* 1.3 51.4 + - - +
69B THR* 2.6 37.1 + - - +
168B ILE* 4.1 9.0 - - + -
198B PHE* 4.0 24.0 - - + -
212B TYR* 3.7 21.0 - - + -
237B TYR* 4.7 0.4 - - - -
242B HIS* 3.2 37.9 - - + +
245B ALA* 4.2 7.2 - - + -
246B PHE* 3.3 39.7 - - + -
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Residues in contact with GLY 66 (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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62B LEU 3.5 3.2 + - - -
63B ALA 3.3 5.6 + - - -
65B MET* 1.3 79.5 - - - +
67B GLY* 1.3 63.2 + - - +
68B CYS 3.2 2.2 - - - -
69B THR* 2.9 19.3 + - - -
70B LYS* 3.3 16.8 + - - +
142B LEU* 3.7 28.0 - - - -
168B ILE* 4.1 7.4 - - - +
212B TYR* 5.1 2.0 - - - -
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Residues in contact with GLY 67 (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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63B ALA 2.9 10.9 + - - -
66B GLY* 1.3 76.1 - - - +
68B CYS* 1.3 57.8 + - - +
69B THR 3.4 0.2 - - - -
70B LYS 3.5 3.2 - - - +
73B LEU* 3.5 27.4 - - - +
93B TYR* 3.5 23.4 - - - -
142B LEU* 4.2 0.6 - - - +
227B LYS* 3.0 30.1 + - - -
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Residues in contact with CYS 68 (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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64B HIS 2.9 17.9 + - - +
67B GLY* 1.3 77.2 - - - +
69B THR* 1.3 60.0 + - - +
70B LYS 3.5 1.6 - - - -
93B TYR* 3.4 18.4 - - - -
223B LEU* 3.7 4.1 - - + +
224B MET* 2.8 36.3 + - - +
227B LYS* 3.6 24.2 - - - -
228B ILE* 3.5 35.9 - - + -
231B LEU* 4.1 2.7 - - - -
237B TYR* 3.8 15.5 - - - +
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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