Contacts of the helix formed by residues 48 - 65 (chain B) in PDB entry 2CAR
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 GLU 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TRP* 4.9 14.0 - - + -
93A GLU* 5.6 1.4 - - - +
94A LYS* 5.1 8.6 + - - -
47B GLY* 1.3 76.3 - - - -
49B PRO* 1.3 75.8 - - + +
50B ASP* 4.5 4.0 - - + +
51B GLU* 3.1 36.7 + - + +
52B ILE* 3.2 8.1 + - - +
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Residues in contact with PRO 49 (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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47B GLY 3.7 3.3 - - - +
48B GLU* 1.3 84.4 - - + +
50B ASP* 1.3 64.9 + - - +
52B ILE* 3.4 9.2 + - + +
53B SER* 3.2 25.6 + - - -
74B CYS* 4.0 25.8 - - + -
76B CYS* 5.3 5.4 - - - -
86B PRO* 4.5 11.4 - - + -
113B TYR* 6.0 1.3 - - - +
115B LEU* 3.8 26.7 - - + -
117B THR* 5.1 5.2 - - - +
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Residues in contact with ASP 50 (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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48B GLU* 3.1 3.5 + - + +
49B PRO* 1.3 80.6 - - - +
51B GLU* 1.3 59.5 + - + +
53B SER* 3.3 3.9 + - - -
54B ILE* 2.9 38.4 + - + +
115B LEU* 6.1 0.5 - - - +
117B THR* 4.9 4.7 + - - +
131B LEU* 3.4 20.7 - - + +
133B ARG* 3.1 40.9 + - - +
135B ARG* 5.5 1.2 + - - -
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Residues in contact with GLU 51 (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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90A TRP* 5.5 2.1 - - - -
47B GLY* 3.9 5.7 - - - -
48B GLU* 3.1 40.7 + - + +
50B ASP* 1.3 74.8 - - + +
52B ILE* 1.3 55.0 - - - +
54B ILE* 3.3 8.1 + - + +
55B GLN* 2.8 54.8 + - + +
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Residues in contact with ILE 52 (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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46A GLN* 4.3 4.5 - - - +
44B GLU* 6.1 0.4 - - - -
45B TYR* 3.3 36.3 - - + +
46B GLN* 3.6 6.5 - - - +
47B GLY* 3.4 35.4 - - - +
48B GLU 3.2 12.9 + - - +
49B PRO* 3.9 4.9 - - + +
51B GLU* 1.3 81.3 - - - +
53B SER* 1.3 57.7 + - - +
55B GLN* 3.3 8.5 + - - +
56B LYS* 2.8 36.6 + - - +
72B ASP* 4.0 17.3 - - - +
86B PRO* 3.5 28.7 - - + -
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Residues in contact with SER 53 (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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49B PRO 3.2 14.3 + - - -
50B ASP 3.7 4.0 - - - -
52B ILE* 1.3 79.4 - - - +
54B ILE* 1.4 59.2 + - - +
56B LYS* 3.8 1.8 - - - +
57B CYS* 2.9 30.8 + - - +
70B VAL* 4.3 1.9 - - - +
72B ASP* 3.2 25.2 + - - +
117B THR* 3.4 34.8 + - - +
119B ALA* 3.7 11.0 - - - +
131B LEU* 3.9 8.3 - - - -
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Residues in contact with ILE 54 (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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50B ASP* 2.9 26.5 + - + +
51B GLU* 3.8 7.2 - - + +
53B SER* 1.4 78.2 - - - +
55B GLN* 1.4 59.2 + - + +
57B CYS* 3.2 2.6 + - - +
58B GLN* 2.8 57.3 + - + +
129B VAL* 4.1 30.1 - - + +
131B LEU* 4.1 19.7 - - + -
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Residues in contact with GLN 55 (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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43A PRO* 4.8 8.3 - - - +
44A GLU 5.2 1.6 + - - +
45B TYR* 3.7 38.2 - - + +
46B GLN 3.3 25.1 + - - +
51B GLU* 2.8 48.6 + - + +
52B ILE* 3.6 8.0 - - - +
54B ILE* 1.4 74.1 - - + +
56B LYS* 1.3 54.4 + - - +
58B GLN* 3.4 13.9 + - - +
59B GLU* 3.1 28.4 + - - +
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Residues in contact with LYS 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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42B LEU* 3.6 28.8 - - + +
43B PRO 3.9 10.8 - - - +
44B GLU* 2.8 32.8 + - - +
45B TYR* 4.0 12.2 - - + -
52B ILE* 2.8 26.3 + - - +
53B SER* 3.8 5.6 - - - +
55B GLN* 1.3 68.9 - - - +
57B CYS* 1.3 66.7 - - - +
59B GLU* 3.3 3.7 + - - +
60B ALA* 2.9 21.8 + - - +
70B VAL* 4.2 17.7 - - + -
71B GLU 4.3 5.1 + - - +
72B ASP* 2.7 34.6 + - - +
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Residues in contact with CYS 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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53B SER 2.9 18.6 + - - +
54B ILE 3.6 3.1 - - - +
56B LYS* 1.3 77.0 - - - +
58B GLN* 1.3 59.7 + - - +
60B ALA* 3.0 6.2 + - - +
61B VAL* 2.7 32.6 + - - +
68B VAL* 4.2 9.6 - - - -
70B VAL* 4.0 8.9 - - + +
119B ALA* 3.7 32.5 - - + -
120B LEU 3.9 2.2 - - - -
121B SER* 3.8 32.3 - - - -
129B VAL* 3.9 11.7 - - + -
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Residues in contact with GLN 58 (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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54B ILE* 2.8 44.9 + - - +
55B GLN* 3.8 11.7 - - - +
57B CYS* 1.3 73.5 - - - +
59B GLU* 1.3 63.7 + - - +
61B VAL* 3.3 9.9 + - - +
62B ARG* 3.0 21.5 + - - +
128B PRO* 5.9 2.2 - - - +
129B VAL* 3.9 18.0 - - + +
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Residues in contact with GLU 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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42B LEU* 3.5 18.2 - - + -
43B PRO* 3.9 15.2 - - + +
45B TYR* 3.7 23.1 + - + +
55B GLN 3.1 10.8 + - - +
56B LYS 3.7 7.9 - - - +
57B CYS 3.2 0.2 - - - -
58B GLN* 1.3 76.9 - - - +
60B ALA* 1.3 61.6 + - - +
62B ARG* 2.5 47.4 + - - +
63B GLN* 3.1 30.7 + - - +
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Residues in contact with ALA 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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13B VAL* 4.5 2.9 - - + -
40B ILE* 5.1 1.6 - - + -
42B LEU* 3.6 24.8 - - + +
56B LYS 2.9 13.8 + - - +
57B CYS 3.0 7.4 + - - +
59B GLU* 1.3 73.5 - - - +
61B VAL* 1.3 55.1 - - - +
63B GLN* 3.1 4.7 + - - +
64B VAL* 2.8 43.1 + - + +
68B VAL* 3.8 25.1 - - + -
70B VAL* 4.1 7.4 - - + -
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Residues in contact with VAL 61 (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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57B CYS 2.7 15.0 + - - +
58B GLN* 3.5 12.1 - - - +
59B GLU 3.2 0.2 - - - -
60B ALA* 1.3 77.2 - - - +
62B ARG* 1.3 63.6 + - - +
64B VAL* 4.7 0.2 - - - -
65B GLN* 2.8 29.4 + - - +
66B GLY 4.7 0.4 - - - -
68B VAL* 3.5 14.4 - - + -
121B SER* 3.3 37.2 - - - +
123B GLY* 4.0 28.9 - - - +
124B ASP 5.6 1.6 - - - +
125B PRO* 5.9 2.7 - - + -
129B VAL* 5.8 0.7 - - + -
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Residues in contact with ARG 62 (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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62A ARG* 6.3 0.8 - - - +
58B GLN 3.0 13.1 + - - +
59B GLU* 2.5 52.9 + - - +
61B VAL* 1.3 76.0 - - - +
63B GLN* 1.3 74.8 + - - +
65B GLN* 3.2 27.1 + - - +
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Residues in contact with GLN 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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40B ILE* 3.7 22.7 - - + +
41B ASP* 2.6 34.0 + - - +
42B LEU* 3.6 7.1 - - - +
43B PRO* 5.3 0.3 - - - +
59B GLU* 3.1 24.9 + - - +
60B ALA 3.1 6.8 + - - +
61B VAL 3.0 0.6 - - - -
62B ARG* 1.3 98.3 - - - +
64B VAL* 1.3 62.4 + - - +
65B GLN* 4.5 3.0 + - - +
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Residues in contact with VAL 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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11B VAL* 4.2 16.6 - - + -
38B GLN* 5.3 0.7 - - - +
40B ILE* 3.8 32.3 - - + -
60B ALA* 2.8 23.1 + - - +
63B GLN* 1.3 74.7 - - - +
65B GLN* 1.3 70.4 + - - +
66B GLY* 3.8 25.6 - - - +
67B PRO 4.1 9.0 - - - +
68B VAL* 4.0 17.0 - - + -
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Residues in contact with GLN 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 VAL* 2.8 18.4 + - - +
62B ARG* 3.2 25.5 + - - +
63B GLN 4.5 3.3 + - - +
64B VAL* 1.3 81.0 - - - +
66B GLY* 1.3 57.5 + - - +
123B GLY* 4.8 6.5 - - - -
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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