Contacts of the helix formed by residues 45 - 59 (chain A) in PDB entry 3CMM
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 LYS 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY 3.6 2.6 + - - -
44A LEU* 1.3 77.1 - - - +
46A GLY* 1.3 70.3 + - - +
47A LEU 3.3 2.0 - - - -
48A GLY 3.1 3.1 + - - +
49A VAL 3.0 17.8 + - - -
74A ALA* 6.3 0.2 - - - +
75A ASP* 3.4 29.0 + - + +
79A GLN* 3.4 12.2 - - - +
91A ARG* 3.5 32.8 - - - +
129A THR* 4.9 1.0 - - - +
130A ASP* 3.9 26.0 - - - +
131A THR* 3.6 22.8 - - + +
358A ASP* 4.8 14.8 + - - -
419A ASN* 5.1 8.3 + - - -
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Residues in contact with GLY 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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45A LYS* 1.3 76.3 - - - +
47A LEU* 1.3 62.3 + - - +
49A VAL* 3.4 3.6 + - - +
50A GLU* 3.1 19.6 + - - +
75A ASP 5.0 1.0 + - - -
78A THR* 3.3 43.7 + - - +
79A GLN* 3.7 7.7 - - - +
358A ASP* 5.0 1.6 + - - -
363A VAL* 3.5 12.4 - - - +
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Residues in contact with LEU 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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45A LYS 3.3 0.6 - - - -
46A GLY* 1.3 73.3 - - - +
48A GLY* 1.3 63.6 + - - +
50A GLU* 3.5 1.2 + - - +
51A ILE* 3.1 40.9 + - + +
129A THR* 4.5 3.1 - - - +
130A ASP* 3.6 21.3 + - - +
154A SER* 3.4 43.7 - - - +
155A GLU* 4.0 13.2 - - - -
156A THR* 4.4 7.4 - - + +
358A ASP* 5.5 0.4 + - - -
363A VAL* 3.7 25.5 - - + +
366A PHE* 3.7 14.6 - - + -
367A GLY 3.7 27.1 - - - +
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Residues in contact with GLY 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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41A ILE* 4.1 7.8 - - - +
43A GLY 3.5 24.2 - - - -
44A LEU* 4.4 4.7 - - - -
45A LYS 3.1 6.3 + - - -
47A LEU* 1.3 80.5 - - - +
49A VAL* 1.3 58.4 + - - +
51A ILE* 3.4 4.6 + - - +
52A ALA* 2.9 29.2 + - - +
129A THR* 3.8 15.4 + - - +
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Residues in contact with VAL 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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44A LEU* 4.6 5.3 - - + +
45A LYS 3.0 7.4 + - - +
46A GLY* 3.4 11.7 - - - +
48A GLY* 1.3 73.9 - - - +
50A GLU* 1.3 64.1 + - - +
52A ALA* 4.1 3.8 - - - -
53A LYS* 2.8 30.3 + - - +
79A GLN* 3.5 37.5 - - + +
80A PHE* 3.8 19.2 - - + -
81A PHE* 3.7 19.7 - - + -
95A THR* 3.4 32.3 - - + -
99A LEU* 4.3 5.2 - - + -
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Residues in contact with GLU 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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46A GLY 3.1 13.5 + - - +
47A LEU 3.7 4.5 - - - +
49A VAL* 1.3 74.6 - - - +
51A ILE* 1.3 68.2 + - - +
53A LYS* 2.7 34.4 + - - +
54A ASN* 3.1 34.1 + - - -
78A THR 5.8 0.2 - - - +
80A PHE* 3.5 11.6 - - + -
363A VAL* 3.9 27.4 - - + +
364A ALA* 4.3 10.2 - - - +
367A GLY* 3.9 11.7 - - - -
368A GLY 4.5 0.2 + - - -
448A GLU* 4.4 0.2 - - - -
451A LYS* 2.6 35.3 + - - -
871A SER* 3.2 14.8 + - - -
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Residues in contact with ILE 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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41A ILE* 3.8 18.4 - - + -
47A LEU* 3.1 38.9 + - + +
48A GLY* 3.8 3.8 - - - +
50A GLU* 1.3 78.5 - - - +
52A ALA* 1.3 64.0 + - - +
54A ASN* 3.2 2.3 + - - +
55A VAL* 2.9 39.6 + - + +
127A VAL* 4.2 9.6 - - + -
129A THR* 4.0 12.6 - - - +
154A SER* 5.1 1.8 - - - -
367A GLY* 3.9 22.2 - - - +
370A VAL* 3.8 29.2 - - + -
371A ALA* 4.1 10.8 - - - +
374A VAL* 4.4 6.7 - - + -
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Residues in contact with ALA 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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41A ILE* 3.6 21.1 - - + -
44A LEU* 5.0 3.4 - - + -
48A GLY 2.9 18.0 + - - +
49A VAL* 3.7 6.1 - - - +
51A ILE* 1.3 77.6 - - - +
53A LYS* 1.3 56.6 + - - +
56A VAL* 2.9 36.6 + - - +
63A MET* 4.3 9.0 - - + -
65A VAL* 5.0 1.1 - - + -
99A LEU* 3.8 29.2 - - + -
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Residues in contact with LYS 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 VAL 2.8 20.8 + - - +
50A GLU* 2.7 39.8 + - - +
52A ALA* 1.3 71.4 - - - +
54A ASN* 1.3 84.5 + - - +
56A VAL 4.0 0.2 - - - -
57A LEU* 3.1 42.2 + - + +
80A PHE* 4.1 12.3 - - + -
99A LEU* 3.9 3.9 - - + +
102A LEU* 3.8 20.6 - - + +
448A GLU* 2.8 29.2 + - - -
451A LYS* 4.1 1.0 - - - +
483A PHE* 3.7 38.4 - - + -
871A SER* 2.9 3.2 + - - -
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Residues in contact with ASN 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 GLU* 3.1 20.8 + - - -
51A ILE 3.7 1.6 - - - +
53A LYS* 1.3 97.8 - - - +
55A VAL* 1.3 61.2 + - - +
57A LEU* 3.7 5.2 + - - +
58A ALA* 3.3 22.0 + - - +
367A GLY 3.7 3.2 + - - -
368A GLY* 3.6 21.4 - - - -
371A ALA* 3.5 19.7 - - + -
375A LEU* 5.2 2.9 - - - +
866A ILE* 6.2 0.2 - - - +
867A ALA* 3.4 25.3 - - + +
868A THR* 4.3 10.3 + - - +
871A SER* 3.2 22.0 + - - -
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Residues in contact with VAL 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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39A VAL* 4.2 2.7 - - + -
41A ILE* 5.2 0.4 - - + -
51A ILE* 2.9 31.1 + - + +
54A ASN* 1.3 73.3 - - - +
56A VAL* 1.3 66.8 + - - +
58A ALA* 3.3 7.9 + - - +
59A GLY 3.2 16.6 + - - -
60A VAL* 3.7 30.2 + - + +
63A MET* 3.6 26.2 - - + -
371A ALA* 3.9 26.5 - - + +
374A VAL* 4.0 23.6 - - + -
375A LEU* 4.5 3.8 - - + -
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Residues in contact with VAL 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 ALA 2.9 23.2 + - - +
53A LYS 4.1 2.5 - - - +
55A VAL* 1.3 75.7 - - - +
57A LEU* 1.3 58.8 + - - +
59A GLY 3.2 4.5 + - - -
60A VAL* 5.1 0.4 - - - -
63A MET* 3.8 35.9 - - + -
99A LEU* 3.9 27.8 - - + +
100A ALA* 5.8 0.2 - - - -
102A LEU* 4.0 9.0 - - + -
103A ASN* 2.9 40.8 + - + +
106A VAL* 3.6 21.3 - - + +
108A VAL* 4.5 7.6 - - + -
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Residues in contact with LEU 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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18A LEU* 5.6 0.5 - - - +
19A TYR* 3.6 2.3 - - - -
53A LYS* 3.1 32.5 + - + +
54A ASN* 4.0 4.0 - - - +
55A VAL 3.2 0.2 - - - -
56A VAL* 1.3 76.0 - - - +
58A ALA* 1.3 61.6 + - - +
59A GLY 3.4 0.7 + - - -
102A LEU* 3.9 36.1 - - + +
103A ASN* 3.5 12.2 + - - +
479A LEU 3.7 22.9 - - - +
480A ASN* 3.2 35.5 + - - +
481A ARG* 4.9 1.6 - - - -
483A PHE* 3.8 24.9 - - + -
867A ALA* 4.1 22.9 - - + -
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Residues in contact with ALA 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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19A TYR* 3.4 7.6 - - - -
22A GLN* 2.8 36.4 + - - +
31A MET* 3.8 2.4 - - - +
34A MET* 3.4 9.5 - - + +
54A ASN 3.3 12.4 + - - +
55A VAL 3.3 9.8 + - - +
57A LEU* 1.3 78.6 - - - +
59A GLY* 1.3 59.6 + - - +
375A LEU* 3.7 36.3 - - + -
866A ILE* 5.1 2.0 - - + -
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Residues in contact with GLY 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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19A TYR* 3.4 19.5 - - - -
34A MET* 4.1 4.5 - - - +
35A GLN* 3.4 30.1 + - - +
55A VAL 3.2 3.0 + - - -
56A VAL 3.2 7.6 + - - -
57A LEU 3.3 0.2 - - - -
58A ALA* 1.3 78.9 - - - +
60A VAL* 1.3 66.2 + - - +
106A VAL* 3.7 15.7 - - - -
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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