Contacts of the helix formed by residues 53 - 66 (chain B) in PDB entry 2H1O
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 GLY 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B LEU 3.4 3.9 + - - -
52B ASN* 1.3 76.2 - - - +
54B LYS* 1.3 62.7 + - - -
55B LYS* 3.1 5.2 + - - -
56B LYS* 3.5 2.8 + - - +
57B ASN* 2.6 37.7 + - - +
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Residues in contact with LYS 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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53B GLY* 1.3 71.4 - - - -
55B LYS* 1.3 63.1 + - - +
57B ASN* 3.1 7.0 + - - +
58B VAL* 2.9 33.8 + - + +
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Residues in contact with LYS 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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50B LEU* 4.4 20.6 - - + -
51B LEU 5.9 1.1 - - - +
53B GLY* 4.9 2.0 - - - -
54B LYS* 1.3 81.6 - - - +
56B LYS* 1.3 65.7 + - - +
58B VAL* 3.9 3.5 - - - +
59B LEU* 3.0 22.8 + - - +
59F ILE* 3.1 29.9 + - + +
60F GLY* 4.2 4.4 + - - -
61F GLY 3.1 17.0 + - - -
62F VAL* 3.3 30.5 - - + +
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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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47B VAL* 3.9 18.8 - - + +
48B ALA* 3.3 28.6 + - - +
50B LEU* 3.1 39.2 + - + +
51B LEU 3.6 16.9 + - - +
52B ASN* 3.4 29.2 + - - +
53B GLY 3.5 7.8 + - - +
55B LYS* 1.3 79.6 - - - +
57B ASN* 1.3 63.7 + - - +
59B LEU* 3.7 2.4 + - - +
60B HIS* 3.1 33.5 + - + +
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Residues in contact with ASN 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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52B ASN* 5.3 6.6 + - - +
53B GLY* 2.6 30.3 + - - +
54B LYS* 3.1 8.8 + - - +
55B LYS 3.1 1.0 - - - -
56B LYS* 1.3 82.3 - - - +
58B VAL* 1.3 64.4 + - + +
60B HIS* 3.6 5.9 + - - +
61B GLU* 3.0 21.7 + - - +
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Residues in contact with VAL 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 LYS* 2.9 28.3 + - + +
55B LYS* 4.0 2.9 - - - +
57B ASN* 1.3 69.9 - - + +
59B LEU* 1.3 66.7 + - - +
61B GLU* 3.1 7.9 - - - +
62B ARG* 2.9 51.9 + - + +
58F GLU* 4.0 7.6 - - + +
59F ILE* 3.9 22.0 - - + -
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Residues in contact with LEU 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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13B LEU* 4.7 17.9 - - + -
47B VAL* 3.9 26.2 - - + -
50B LEU* 3.7 25.6 - - + -
55B LYS 3.0 16.9 + - - +
56B LYS 3.8 4.0 - - - +
58B VAL* 1.3 78.9 - - - +
60B HIS* 1.3 52.4 + - - +
62B ARG* 3.2 4.9 + - - +
63B MET* 2.7 42.8 + - + +
67B ILE* 6.2 1.6 - - + -
55F ILE* 4.8 7.0 - - + -
59F ILE* 3.7 31.5 - - + +
62F VAL* 4.0 15.7 - - + -
64F LEU* 5.3 4.3 - - + -
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Residues in contact with HIS 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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47B VAL* 3.9 22.9 - - + +
48B ALA* 6.2 1.8 - - + -
56B LYS* 3.1 23.9 + - + +
57B ASN* 3.7 7.4 - - - +
59B LEU* 1.3 77.9 - - - +
61B GLU* 1.3 67.4 + - - +
63B MET* 3.2 4.5 + - - +
64B GLU* 3.0 46.6 + - + +
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Residues in contact with GLU 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 ASN 3.0 12.5 + - - +
58B VAL* 3.1 13.2 - - - +
60B HIS* 1.3 83.6 + - - +
62B ARG* 1.3 71.3 + - - +
64B GLU* 3.4 1.0 + - - +
65B GLN* 2.8 75.3 + - + +
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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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58B VAL* 2.9 24.9 + - + +
59B LEU* 3.5 6.3 - - + +
61B GLU* 1.3 106.0 - - - +
63B MET* 1.3 66.1 + - - +
66B SER* 2.6 45.3 + - - -
67B ILE* 3.1 8.0 + - + -
55F ILE* 3.8 43.4 - - + +
58F GLU* 2.8 36.2 + - - +
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Residues in contact with MET 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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13B LEU* 5.2 4.0 - - + -
43B MET* 3.6 38.1 - - + +
44B ARG* 5.1 4.0 - - + -
47B VAL* 3.5 30.3 - - + -
59B LEU* 2.7 28.0 + - + +
60B HIS* 3.4 9.6 - - + +
62B ARG* 1.3 72.4 - - - +
64B GLU* 1.3 72.5 + - - +
67B ILE* 3.7 14.3 - - - +
68B LEU* 3.0 57.2 + - + +
64F LEU* 3.8 13.2 - - + -
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Residues in contact with GLU 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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44B ARG* 2.9 44.0 + - - -
60B HIS* 3.0 45.0 + - + +
61B GLU* 4.0 2.0 - - - +
63B MET* 1.3 85.5 - - - +
65B GLN* 1.3 70.6 + - + +
66B SER 3.7 0.2 - - - -
68B LEU* 3.8 11.3 - - - +
69B PRO* 3.0 19.0 - - - +
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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 GLU* 2.8 58.2 + - + +
64B GLU* 1.3 83.1 + - + +
66B SER* 1.3 61.5 + - - +
69B PRO* 3.1 18.4 - - - +
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Residues in contact with SER 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 ARG* 2.6 36.5 + - - -
64B GLU 3.7 0.2 - - - -
65B GLN* 1.3 77.6 - - - +
67B ILE* 1.3 68.1 + - - +
69B PRO* 3.4 7.3 - - - +
70B LEU* 3.4 19.6 + - - +
51F MET* 4.0 19.3 - - - +
55F ILE* 4.3 7.6 - - - -
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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