Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 2H1C
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 ASN 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.3 1.9 - - - +
51A LEU* 1.3 75.6 - - - +
53A GLY* 1.3 64.6 + - - +
54A LYS* 2.9 14.1 + - - +
55A LYS* 2.8 46.9 + - + +
56A LYS* 2.9 23.6 + - - +
140A ACT 3.1 16.8 + - + +
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Residues in contact with GLY 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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50A LEU 5.6 0.4 - - - -
51A LEU 3.6 5.1 + - - -
52A ASN* 1.3 71.8 + - - +
54A LYS* 1.3 62.3 + - - +
56A LYS* 3.3 11.7 + - - +
57A ASN* 3.0 32.8 + - - +
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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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52A ASN* 2.9 9.4 + - - +
53A GLY* 1.3 76.0 - - - +
55A LYS* 1.3 64.2 + - - +
57A ASN* 3.3 6.6 + - + +
58A VAL* 3.1 29.8 + - + +
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Residues in contact with LYS 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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50A LEU* 4.1 7.4 - - + -
52A ASN* 2.8 39.0 + - + +
54A LYS* 1.3 73.1 - - - +
56A LYS* 1.3 59.0 + - - +
58A VAL* 3.4 5.4 + - - +
59A LEU* 2.8 29.3 + - + +
140A ACT 5.0 8.5 - - - +
59B ILE* 2.6 48.6 + - + +
60B GLY* 3.7 8.5 + - - -
61B GLY 3.2 19.1 + - - -
62B VAL* 3.7 24.7 - - + -
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Residues in contact with LYS 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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47A VAL* 3.3 29.1 - - + +
48A ALA* 3.8 21.9 + - - +
50A LEU* 3.8 25.8 + - + +
52A ASN 2.9 16.8 + - - +
53A GLY* 3.6 9.4 - - - +
55A LYS* 1.3 76.9 - - - +
57A ASN* 1.3 70.5 + - - +
59A LEU 3.8 0.2 - - - -
60A HIS* 2.8 35.6 + - + +
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Residues in contact with ASN 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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53A GLY* 3.0 26.0 + - - +
54A LYS* 3.7 7.2 - - + +
55A LYS 3.3 0.2 - - - -
56A LYS* 1.3 89.7 - - - +
58A VAL* 1.3 63.7 + - + +
60A HIS* 3.6 6.6 + - - +
61A GLU* 3.1 22.2 + - - +
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Residues in contact with VAL 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* 3.1 19.4 + - + +
55A LYS* 3.8 4.0 - - - +
57A ASN* 1.3 78.4 - - + +
59A LEU* 1.3 57.7 + - - +
61A GLU* 3.2 8.2 + - - +
62A ARG* 3.0 41.8 + - + +
58B GLU* 4.5 11.2 - - - +
59B ILE* 3.6 24.0 - - + -
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Residues in contact with LEU 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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13A LEU* 4.7 14.6 - - + -
47A VAL* 3.7 30.3 - - + -
50A LEU* 3.8 15.5 - - + -
55A LYS 2.8 21.6 + - - +
56A LYS 4.1 2.0 - - - +
58A VAL* 1.3 72.3 - - - +
60A HIS* 1.3 61.0 + - - +
62A ARG* 4.3 4.5 - - + +
63A LEU* 2.8 35.9 + - + +
67A ILE* 5.1 3.8 - - + -
55B ILE* 4.2 23.3 - - + -
59B ILE* 4.1 13.0 - - + -
62B VAL* 3.6 30.7 - - + -
64B LEU* 4.2 5.4 - - + -
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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
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47A VAL* 3.8 11.4 - - + +
56A LYS* 2.8 22.4 + - + +
57A ASN* 3.6 7.3 + - - +
59A LEU* 1.3 76.5 - - - +
61A GLU* 1.3 67.5 + - - +
63A LEU* 3.3 4.7 + - + +
64A GLU* 3.0 57.4 + - + +
204A MG 3.9 20.0 - - - -
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Residues in contact with GLU 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 ASN 3.1 10.2 + - - +
58A VAL* 3.4 11.2 - - - +
60A HIS* 1.3 85.0 + - - +
62A ARG* 1.3 77.8 + - - +
64A GLU* 5.0 1.8 - - - -
65A GLN* 2.8 69.2 + - + +
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Residues in contact with ARG 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 VAL* 3.0 28.2 + - + +
59A LEU* 3.3 5.8 + - + +
61A GLU* 1.3 101.6 - - - +
63A LEU* 1.3 61.0 + - - +
66A SER* 2.9 26.2 + - - -
67A ILE* 2.9 28.2 + - - +
55B ILE* 3.5 40.6 - - + +
58B GLU* 2.8 36.2 + - - +
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Residues in contact with LEU 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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13A LEU* 6.4 0.9 - - + -
40A VAL* 6.2 0.2 - - + -
43A LEU* 4.3 17.7 - - + -
44A ARG* 3.8 42.2 - - + +
47A VAL* 4.1 18.8 - - + -
59A LEU* 2.8 22.8 + - + +
60A HIS* 3.7 5.4 - - + +
62A ARG* 1.3 75.1 - - - +
64A GLU* 1.3 64.3 + - - +
67A ILE* 4.0 30.9 - - + +
68A LEU* 2.9 53.1 + - + +
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Residues in contact with GLU 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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44A ARG* 2.9 54.2 + - - +
60A HIS* 3.0 48.1 + - + +
61A GLU* 4.2 1.1 - - - +
63A LEU* 1.3 83.7 - - + +
65A GLN* 1.3 72.1 + - + +
68A LEU* 3.5 9.1 - - - +
69A PRO* 3.4 18.9 - - - +
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Residues in contact with GLN 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 GLU* 2.8 45.4 + - + +
64A GLU* 1.3 87.4 - - + +
66A SER* 1.3 60.9 + - - +
69A PRO* 3.6 13.6 - - - +
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Residues in contact with SER 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 ARG* 2.9 34.8 + - - -
65A GLN* 1.3 83.9 + - - +
67A ILE* 1.3 68.1 + - - +
69A PRO* 3.6 7.0 - - - +
70A LEU* 3.5 20.6 + - - +
51B MET* 4.4 8.3 - - - +
55B ILE* 5.0 5.8 - - - -
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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