Contacts of the helix formed by residues 48 - 68 (chain A) in PDB entry 3CMQ
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 HIS 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.7 30.4 + - + +
45A GLN* 2.9 42.2 + - - +
46A GLN 3.2 2.2 + - - -
47A HIS* 1.3 77.9 - - - +
49A PRO* 1.3 78.9 - - + +
50A LEU* 3.2 50.0 + - + +
51A TRP* 2.8 19.6 + - - +
52A LEU* 2.8 12.0 + - - +
296A PHE* 2.9 34.6 + + - -
304A LEU* 4.2 13.1 - - + +
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Residues in contact with PRO 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS 3.5 1.3 - - - +
48A HIS* 1.3 105.1 - - + +
50A LEU* 1.3 55.9 + - - +
52A LEU* 3.3 10.0 + - + +
53A ILE* 3.0 32.6 + - - +
284A ALA* 5.1 0.7 - - + -
288A TYR* 4.2 9.1 - - + -
296A PHE* 3.8 22.2 - - + -
303A PHE* 3.9 18.8 - - + -
304A LEU* 4.6 3.4 - - + -
307A PHE* 3.8 43.5 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.3 6.5 - - + -
43A HIS* 4.3 15.6 - - + -
48A HIS* 3.2 26.9 + - + +
49A PRO* 1.3 73.5 - - - +
51A TRP* 1.3 65.1 + - - +
53A ILE* 3.4 5.2 + - + +
54A LYS* 3.0 23.4 + - - +
156A HIS* 3.5 34.8 - - + +
280A LEU* 3.9 42.4 - - + +
281A GLU* 3.6 15.3 - - + +
284A ALA* 4.2 3.8 - - + -
296A PHE* 3.9 23.1 - - + -
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Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 4.0 5.3 + - - +
43A HIS 3.4 26.0 - - - +
44A ASN* 3.9 14.7 + - - -
45A GLN 3.0 24.7 - - - +
46A GLN* 3.9 24.8 - - + +
47A HIS* 3.1 38.6 - + - -
48A HIS 2.8 6.4 + - - +
50A LEU* 1.3 78.0 - - - +
52A LEU* 1.3 90.3 + - + +
54A LYS* 3.3 10.9 + - - +
55A GLU* 2.9 51.7 + - + +
307A PHE 5.6 0.2 - - - -
309A VAL* 5.8 2.0 - - + -
312A ILE* 4.2 17.5 - - + -
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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
----------------------------------------------------------
47A HIS 5.4 0.7 - - - +
48A HIS 2.8 11.7 + - - +
49A PRO* 3.3 10.3 - - + +
50A LEU 3.2 0.2 - - - -
51A TRP* 1.3 89.6 - - + +
53A ILE* 1.3 66.2 + - - +
55A GLU* 3.2 2.9 + - - +
56A ARG* 3.0 34.3 + - - +
288A TYR* 3.0 29.4 - - + +
307A PHE* 4.3 20.4 - - + +
309A VAL* 4.2 14.4 - - + -
312A ILE* 3.9 38.8 - - + +
314A GLN 5.7 0.7 - - - +
316A VAL* 4.1 16.4 - - + -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO 3.0 17.2 + - - +
50A LEU* 3.7 8.1 - - + +
52A LEU* 1.3 74.1 - - - +
54A LYS* 1.3 65.6 + - - +
56A ARG* 3.1 8.5 + - - +
57A VAL* 2.9 38.2 + - + +
218A LEU* 5.1 7.2 - - + -
280A LEU* 3.7 28.0 - - + +
283A LEU* 4.4 17.7 - - + -
284A ALA* 4.1 24.9 - - + +
287A LEU* 3.4 34.3 - - + -
288A TYR* 4.0 9.6 - - + +
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Residues in contact with LYS 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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43A HIS* 2.9 17.8 + - + +
44A ASN* 2.6 32.5 + - - +
50A LEU 3.0 14.9 + - - +
51A TRP* 3.4 13.9 - - - +
53A ILE* 1.3 78.6 - - - +
55A GLU* 1.3 79.6 + - - +
57A VAL* 3.3 7.9 + - - +
58A LYS* 3.0 36.3 + - + +
78A ASP* 2.8 21.3 + - + +
138A VAL* 3.7 42.6 - - + -
158A LEU* 4.6 6.4 - - + +
280A LEU* 5.0 3.1 - - + +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 2.9 50.6 + - + +
52A LEU* 3.7 4.3 - - - +
53A ILE 3.2 0.2 - - - -
54A LYS* 1.3 92.2 + - - +
56A ARG* 1.3 61.0 + - - +
58A LYS* 3.0 37.0 + - - +
59A GLU* 2.9 30.1 + - - +
312A ILE* 3.9 24.4 - - + +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.0 31.8 + - + +
53A ILE* 3.8 2.7 - - - +
55A GLU* 1.3 76.1 - - - +
57A VAL* 1.3 61.7 + - - +
59A GLU* 3.9 1.7 - - - +
60A HIS 3.2 9.4 + - - -
217A HIS* 2.9 63.6 + - - +
218A LEU* 3.4 40.0 + - + +
287A LEU* 3.9 21.2 - - - +
288A TYR* 4.6 7.0 + - - -
312A ILE* 3.3 41.9 + - + +
313A ASN* 4.7 9.8 + - - +
315A LYS* 5.9 1.6 - - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 2.9 35.0 + - + +
54A LYS 3.6 4.9 - - - +
56A ARG* 1.3 76.7 - - - +
58A LYS* 1.3 64.2 + - - +
60A HIS* 3.2 2.6 + - - +
61A PHE* 3.1 51.1 + - + -
136A LEU* 4.6 2.5 - - + -
158A LEU* 3.6 31.0 - - + -
214A LEU* 4.1 18.4 - - + -
218A LEU* 4.2 20.0 - - + -
278A LEU* 5.2 6.3 - - + -
283A LEU* 5.5 0.2 - - + -
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Residues in contact with LYS 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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54A LYS* 3.0 31.4 + - + +
55A GLU* 3.0 40.9 + - - +
57A VAL* 1.3 78.5 - - + +
59A GLU* 1.3 56.7 + - - +
61A PHE* 3.2 7.8 + - - +
62A TYR* 2.9 28.6 + - - +
76A VAL* 4.1 36.9 - - + +
78A ASP* 4.7 8.7 + - - -
136A LEU* 4.6 9.0 - - + -
158A LEU* 5.9 0.7 - - + -
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Residues in contact with GLU 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 GLU 2.9 16.5 + - - +
56A ARG* 3.9 4.8 - - - +
58A LYS* 1.3 76.0 - - - +
60A HIS* 1.3 58.0 + - - +
62A TYR* 3.2 10.5 + - + +
63A LYS* 2.9 48.5 + - + +
217A HIS* 4.2 9.1 + - - +
312A ILE* 3.8 18.9 - - + +
313A ASN* 3.0 39.4 + - - +
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG 3.2 12.6 + - - +
57A VAL 3.4 8.1 - - - +
58A LYS 3.2 0.2 - - - -
59A GLU* 1.3 80.6 - - - +
61A PHE* 1.3 70.4 + + - +
63A LYS* 3.4 8.7 + - - +
64A GLN* 3.0 56.4 + - + +
210A THR* 4.3 5.0 + - + +
213A ARG* 3.4 31.9 + - + +
214A LEU* 3.6 37.5 + - + +
217A HIS* 3.6 31.2 + + + +
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.1 42.6 + - + -
58A LYS* 3.7 7.9 - - - +
60A HIS* 1.3 84.8 - + - +
62A TYR* 1.3 65.6 + - - +
64A GLN* 3.5 8.8 + - + +
65A TYR* 3.0 23.0 + - - +
71A THR* 4.6 3.2 - - + +
72A PRO 5.1 0.9 - - - +
74A PHE* 3.6 53.5 + + + -
136A LEU* 4.0 21.3 - - + -
160A ALA* 5.0 0.2 - - + -
210A THR* 4.0 25.6 - - + -
214A LEU* 4.2 16.2 - - + -
274A TRP* 4.9 0.9 - + - -
276A PHE* 4.0 23.3 - + - -
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Residues in contact with TYR 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 LYS 2.9 13.6 + - - +
59A GLU* 3.5 14.4 - - + +
61A PHE* 1.3 77.2 - - - +
63A LYS* 1.3 73.6 + - + +
65A TYR* 2.9 28.0 + + - +
66A VAL* 3.0 38.7 + - + +
73A LEU* 5.1 9.4 - - + -
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Residues in contact with LYS 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 GLU* 2.9 41.9 + - + +
60A HIS* 3.7 9.7 + - - +
62A TYR* 1.3 86.1 - - + +
64A GLN* 1.3 57.1 + - - +
66A VAL* 3.2 6.1 + - - +
67A GLY* 2.7 34.1 + - - -
217A HIS* 4.3 20.1 + - + -
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Residues in contact with GLN 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 HIS* 3.0 45.0 + - + +
61A PHE* 3.8 9.4 - - + +
62A TYR 3.2 0.2 - - - -
63A LYS* 1.3 81.4 - - - +
65A TYR* 1.3 57.7 + - - +
67A GLY* 4.3 1.5 - - - +
68A ARG* 2.9 56.8 + - - +
71A THR* 3.1 25.9 + - + +
213A ARG* 2.8 38.4 - - - +
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Residues in contact with TYR 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 PHE 3.0 13.8 + - - +
62A TYR* 2.9 17.8 + + - +
64A GLN* 1.3 78.2 - - - +
66A VAL* 1.3 77.1 + - + +
68A ARG 3.4 14.4 - - - +
69A PHE* 5.2 0.3 - - - -
71A THR* 3.3 28.2 - - - +
72A PRO* 4.0 8.3 - - + +
73A LEU* 3.5 55.6 - - + +
74A PHE 5.6 0.2 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 3.0 52.8 + - + +
63A LYS* 3.9 5.6 - - - +
65A TYR* 1.3 88.3 - - + +
67A GLY* 1.3 61.9 + - - +
68A ARG 5.2 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 LYS 2.7 20.4 + - - -
64A GLN* 3.9 1.8 - - - -
65A TYR 3.3 0.2 - - - -
66A VAL* 1.3 76.7 - - - +
68A ARG* 1.3 65.0 + - - +
69A PHE 4.3 0.7 + - - -
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 2.9 42.4 + - - +
65A TYR 3.4 15.1 - - - +
66A VAL 5.2 0.2 - - - -
67A GLY* 1.3 82.6 + - - +
69A PHE* 1.3 66.7 + - - +
70A GLY* 4.3 2.7 - - - +
71A THR* 3.1 33.8 + - - +
213A ARG* 3.7 28.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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