Contacts of the helix formed by residues 60 - 70 (chain B) in PDB entry 2W4G
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 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASN* 3.8 13.2 - - - +
59B VAL* 1.3 76.7 - - - +
61B ASN* 1.3 67.6 + - - +
62B GLU* 4.6 9.4 - - + +
63B GLU* 2.9 44.8 + - - +
64B LEU* 3.5 6.5 + - - +
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Residues in contact with ASN 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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48B ARG* 2.6 34.8 + - - -
59B VAL 4.0 1.6 + - - -
60B LYS* 1.3 68.7 - - - +
62B GLU* 1.3 58.7 + - + +
64B LEU* 3.0 12.4 + - - +
65B ASP* 2.8 41.8 + - - +
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Residues in contact with GLU 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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60B LYS* 3.1 8.1 + - + +
61B ASN* 1.3 75.3 - - + +
63B GLU* 1.3 59.5 + - + +
65B ASP* 3.8 7.1 - - - +
66B ALA* 2.9 29.6 + - - +
69B LYS* 4.9 4.4 + - - +
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Residues in contact with GLU 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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51B PHE* 6.3 0.2 - - - -
58B ASN 4.4 1.4 - - - +
59B VAL* 3.8 12.2 - - + +
60B LYS* 2.9 51.4 + - - +
62B GLU* 1.3 74.7 - - + +
64B LEU* 1.3 65.6 + - - +
66B ALA* 3.3 7.5 + - - +
67B MET* 3.1 29.1 + - - +
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Residues in contact with LEU 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 LYS* 4.0 9.9 - - + +
47B LEU* 3.7 18.5 - - + +
48B ARG* 3.4 47.8 - - + +
51B PHE* 3.7 28.3 - - + -
59B VAL* 3.7 22.7 - - + +
60B LYS 4.2 0.2 - - - -
61B ASN* 3.0 26.4 + - - +
63B GLU* 1.3 75.5 - - - +
65B ASP* 1.3 65.8 + - - +
67B MET* 3.3 12.1 - - - +
68B ILE* 3.1 27.3 + - - +
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Residues in contact with ASP 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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44B LYS* 2.6 42.2 + - - +
61B ASN* 2.8 38.7 + - - +
62B GLU* 3.8 8.3 - - - +
64B LEU* 1.3 75.4 - - - +
66B ALA* 1.3 57.0 + - - +
68B ILE* 3.2 4.2 + - - +
69B LYS* 2.9 52.9 + - + +
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Residues in contact with ALA 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 GLU 2.9 22.5 + - - +
63B GLU* 3.3 9.2 + - - +
65B ASP* 1.3 71.3 - - - +
67B MET* 1.3 66.1 + - - +
69B LYS* 3.5 24.7 + - - +
70B GLU* 3.7 11.1 + - - +
830M PRO* 6.1 2.7 - - + -
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Residues in contact with MET 67 (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 LEU* 4.1 13.0 - - + -
51B PHE* 4.8 13.5 - - + -
63B GLU 3.1 17.3 - - - +
64B LEU* 3.3 13.0 - - - +
66B ALA* 1.3 79.3 - - - +
68B ILE* 1.3 64.2 + - - +
70B GLU* 3.4 11.5 + - - +
830M PRO* 2.8 44.9 - - + +
831M TRP* 3.2 61.6 + - + +
834M LEU* 4.7 14.8 - - + -
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Residues in contact with ILE 68 (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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43B ASP* 3.8 9.6 - - + +
44B LYS* 3.5 54.5 - - + +
47B LEU* 4.0 9.9 - - + -
64B LEU 3.1 11.4 + - - +
65B ASP* 3.8 5.4 - - - +
67B MET* 1.3 78.6 - - - +
69B LYS* 1.3 60.7 + - + +
70B GLU 2.9 7.3 + - - -
71B ALA* 3.0 22.2 + - - +
75B ILE* 3.7 31.3 - - + +
831M TRP* 4.8 0.4 - - + -
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Residues in contact with LYS 69 (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 GLU* 4.9 4.4 + - - +
65B ASP* 2.9 51.8 + - - +
66B ALA* 3.6 14.5 - - - +
67B MET 3.4 0.4 - - - -
68B ILE* 1.3 71.9 - - + +
70B GLU* 1.3 61.4 + - - +
71B ALA 3.2 8.8 + - - +
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Residues in contact with GLU 70 (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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66B ALA 3.9 9.2 - - - +
67B MET* 3.6 13.0 - - - +
68B ILE 2.9 1.2 + - - -
69B LYS* 1.3 77.2 - - - +
71B ALA* 1.3 58.0 + - - +
72B SER 4.3 0.2 + - - -
83B MET* 3.1 29.3 - - + +
84B PHE* 5.2 0.3 - - - -
87B LYS* 2.5 22.6 + - - -
829M TRP* 2.4 28.6 + - - -
830M PRO* 4.8 4.0 - - - +
831M TRP* 2.8 25.8 + - + +
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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