Contacts of the helix formed by residues 54 - 67 (chain B) in PDB entry 2W77
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 ALA 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLN* 1.3 76.9 - - - +
55B LEU* 1.3 66.8 + - - +
56B GLY* 4.6 3.4 - - - +
57B SER* 3.0 24.9 + - - +
58B ALA* 3.1 9.7 + - - +
80B LYS 3.7 8.1 - - - +
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Residues in contact with LEU 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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53B GLN 3.1 4.4 + - - -
54B ALA* 1.3 69.0 - - - +
56B GLY* 1.3 64.0 + - - +
58B ALA* 3.1 5.3 + - - +
59B LEU* 2.9 40.3 + - + +
77B VAL* 4.0 23.9 + - + +
80B LYS* 2.9 39.8 + - + +
81B ARG 4.4 0.9 - - - +
82B SER* 4.2 9.2 - - - +
98B LEU* 4.0 13.0 - - + -
99B LEU* 3.6 27.6 - - + -
102B THR* 3.5 31.0 - - + +
104B ALA* 5.1 4.3 - - + -
115B ILE* 5.5 0.4 - - + -
117B VAL* 6.4 0.9 - - + -
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Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 3.1 3.6 + - - +
55B LEU* 1.3 78.8 - - - +
57B SER* 1.3 61.0 + - - +
59B LEU* 3.4 5.9 + - - +
60B GLN* 3.4 26.3 + - - +
72B TYR* 3.7 10.6 + - - -
77B VAL* 4.2 24.4 + - - -
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Residues in contact with SER 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 GLN* 3.5 14.5 + - - +
54B ALA* 3.0 21.6 + - - +
56B GLY* 1.3 74.2 - - - +
58B ALA* 1.3 60.6 + - - +
60B GLN* 3.4 15.7 + - - +
61B GLU* 2.9 27.7 + - - +
64B ARG* 5.4 0.5 + - - -
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Residues in contact with ALA 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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50B ILE* 4.1 13.1 - - + +
53B GLN* 3.6 16.7 + - + -
54B ALA 3.1 12.3 + - - +
55B LEU* 3.3 10.5 - - + +
57B SER* 1.3 77.5 + - - +
59B LEU* 1.3 51.6 + - - +
61B GLU* 2.9 5.4 + - - +
62B PHE* 2.7 34.6 + - - +
82B SER* 3.6 31.4 - - - +
98B LEU* 4.4 7.1 - - + +
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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
----------------------------------------------------------
55B LEU* 2.9 44.6 + - + +
56B GLY* 3.6 5.8 - - - +
58B ALA* 1.3 76.1 - - - +
60B GLN* 1.3 60.3 + - - +
62B PHE* 3.2 6.7 + - - +
63B GLY 3.1 17.8 + - - -
70B VAL* 3.7 16.7 - - + +
72B TYR* 3.7 38.6 - - + -
77B VAL* 4.3 5.6 - - + -
95B ILE* 3.7 19.5 - - + -
98B LEU* 4.1 5.2 - - + -
99B LEU* 4.1 0.7 - - + -
115B ILE* 3.7 39.3 - - + -
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Residues in contact with GLN 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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56B GLY 3.4 10.2 + - - +
57B SER* 3.7 16.7 - - - +
58B ALA 3.3 0.4 - - - -
59B LEU* 1.3 76.4 - - - +
61B GLU* 1.3 62.2 + - - +
63B GLY* 3.4 3.3 + - - -
64B ARG* 3.3 41.0 + - - +
70B VAL* 5.9 0.4 - - - -
72B TYR* 3.4 30.0 + - + +
303B GLU* 6.0 2.2 - - - +
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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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49B ASP 4.8 1.9 - - - +
50B ILE* 3.9 15.0 - - + -
53B GLN* 5.1 6.6 + - - +
57B SER 2.9 15.4 + - - +
58B ALA* 2.9 10.5 + - - +
60B GLN* 1.3 73.8 - - - +
62B PHE* 1.3 65.6 + - - +
63B GLY 3.1 0.2 - - - -
64B ARG* 3.0 42.1 + - - +
65B GLN* 3.0 50.7 + - - +
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Residues in contact with PHE 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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48B PHE* 3.3 32.1 - + - -
50B ILE* 3.7 9.3 - - + +
58B ALA 2.7 16.5 + - - +
59B LEU* 3.3 13.5 - - - +
61B GLU* 1.3 72.0 - - - +
63B GLY* 1.3 63.2 + - - +
65B GLN* 3.5 1.7 + - - +
66B ALA* 3.2 30.1 + - + +
68B ILE* 4.7 7.2 - - + -
70B VAL* 4.1 13.9 - - + -
85B ILE* 4.0 13.9 - - + -
91B PRO* 3.6 16.8 - - + -
94B ALA* 3.5 16.6 - - + -
95B ILE* 3.5 45.1 - - + -
98B LEU* 4.2 9.0 - - + -
113B ILE* 4.0 10.1 - - + -
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Residues in contact with GLY 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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59B LEU 3.1 11.7 + - - -
60B GLN* 3.4 5.8 + - - -
61B GLU 3.1 0.4 - - - -
62B PHE* 1.3 76.0 - - - +
64B ARG* 1.3 56.9 + - - +
67B ASP* 2.9 32.6 + - - -
68B ILE 3.3 21.5 + - - +
69B GLN* 5.3 0.7 - - - -
70B VAL* 4.1 9.0 - - - -
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Residues in contact with ARG 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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57B SER 5.4 0.6 + - - -
60B GLN* 3.3 38.3 + - - +
61B GLU* 3.0 52.1 + - - +
63B GLY* 1.3 77.6 - - - +
65B GLN* 1.3 61.6 + - + +
66B ALA 3.5 0.2 + - - -
67B ASP* 3.7 8.5 + - - +
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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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46B VAL* 3.3 18.8 - - - +
47B GLU 4.5 6.6 - - - +
48B PHE* 3.3 22.1 - - + -
49B ASP* 2.9 48.3 + - - +
50B ILE* 3.6 12.0 - - - +
61B GLU* 3.0 40.4 + - - +
62B PHE 4.2 1.1 - - - +
64B ARG* 1.3 76.8 - - + +
66B ALA* 1.3 58.5 + - - +
67B ASP 3.5 0.2 - - - -
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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
----------------------------------------------------------
46B VAL* 4.3 14.8 - - + +
48B PHE* 4.1 19.3 - - + -
62B PHE* 3.2 28.9 + - + +
65B GLN* 1.3 77.0 - - - +
67B ASP* 1.3 70.2 + - - +
68B ILE* 3.3 17.6 + - + +
91B PRO* 5.2 6.5 - - + -
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Residues in contact with ASP 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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63B GLY 2.9 10.6 + - - -
64B ARG 3.7 6.1 + - - +
65B GLN 3.5 1.8 - - - -
66B ALA* 1.3 81.7 - - - +
68B ILE* 1.3 66.4 + - - +
774B LYS* 3.7 22.0 + - - -
815B PHE 5.3 4.3 - - - +
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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