Contacts of the helix formed by residues 60 - 79 (chain B) in PDB entry 2WWA
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 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 4.4 3.8 - - + -
56B ILE* 3.1 20.3 + - + +
57B GLY* 4.6 6.1 - - - -
59B ILE* 1.4 77.1 - - - +
61B VAL* 1.4 59.8 + - + +
62B GLY 3.6 0.2 + - - -
63B ILE* 3.8 6.5 - - - +
64B ILE* 3.4 32.0 - - + +
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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
----------------------------------------------------------
186A THR 5.9 0.2 - - - +
189A ILE* 4.2 16.2 - - + +
190A ALA* 3.1 41.8 - - + +
193A LEU* 3.8 33.4 - - + -
194A VAL* 3.4 32.6 - - + +
57B GLY 3.2 22.9 - - - +
58B PHE* 3.7 13.0 - - + +
59B ILE 3.9 0.2 - - - +
60B ALA* 1.4 77.5 - - + +
62B GLY* 1.4 57.7 + - - +
63B ILE 3.3 4.5 + - - -
64B ILE 3.5 4.9 + - - -
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Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.9 18.3 - - - +
198A PHE* 6.0 0.9 - - - -
58B PHE* 3.1 19.4 + - - -
59B ILE* 3.4 11.0 - - - -
60B ALA 3.3 1.6 - - - -
61B VAL* 1.4 75.9 - - - +
63B ILE* 1.4 57.7 + - - +
66B TYR* 3.5 18.7 - - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 5.2 0.3 - - - +
59B ILE* 3.5 17.5 + - + +
60B ALA* 3.8 10.1 - - - +
62B GLY* 1.4 76.7 - - - +
64B ILE* 1.4 71.4 + - + +
65B GLY 3.7 0.7 - - - -
66B TYR* 4.1 9.5 - - + +
67B ALA* 3.4 23.2 + - + +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 5.3 5.8 - - - +
41A LEU* 6.5 0.4 - - + -
43A TYR* 5.6 2.0 - - + -
44A LEU* 3.3 36.2 - - + +
187A VAL* 3.9 23.8 - - + +
190A ALA* 3.5 27.6 - - + +
191A THR* 3.6 20.0 - - - +
60B ALA* 3.4 23.6 - - + +
61B VAL 3.5 0.8 + - - -
63B ILE* 1.4 85.1 - - + +
65B GLY* 1.4 63.4 + - - +
66B TYR 3.2 0.6 + - - -
67B ALA 3.5 5.7 + - - -
68B ILE* 3.4 10.0 - - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA 3.4 11.4 + - - -
191A THR* 3.7 26.2 - - - -
194A VAL* 3.7 11.0 - - - -
195A ALA* 4.4 9.6 - - - +
61B VAL 3.5 2.8 + - - -
64B ILE* 1.4 75.9 - - - +
66B TYR* 1.4 61.4 + - - +
68B ILE* 4.0 7.4 - - - +
69B LYS* 3.4 23.0 + - - +
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.5 9.0 - - + +
198A PHE* 3.7 36.2 - + - -
199A GLY* 4.7 8.7 - - - -
200A VAL* 6.0 1.8 - - + -
62B GLY 3.5 23.6 - - - +
63B ILE* 4.1 9.0 - - + +
64B ILE 3.2 0.2 - - - -
65B GLY* 1.4 76.6 - - - +
67B ALA* 1.4 64.3 + - - +
69B LYS* 3.4 4.8 + - + +
70B LEU* 3.2 63.8 + - + +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.3 21.3 - - + -
63B ILE* 3.4 19.1 + - + +
64B ILE 3.8 5.4 - - - +
66B TYR* 1.4 82.0 - - - +
68B ILE* 1.4 60.3 + - - +
70B LEU* 3.8 6.6 + - - +
71B ILE* 3.4 23.1 + - - +
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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
----------------------------------------------------------
43A TYR* 5.9 0.2 - - + -
44A LEU* 3.3 36.1 - - + +
46A ALA* 4.6 8.5 - - + -
47A GLN* 3.7 29.2 - - + +
75A GLU* 4.7 9.6 - - - +
191A THR* 3.6 37.7 - - + +
64B ILE 3.4 17.9 + - - +
65B GLY* 4.0 6.1 - - - +
67B ALA* 1.4 75.7 - - - +
69B LYS* 1.4 62.1 + - + +
71B ILE* 3.5 6.7 - - - +
72B HIS* 3.2 25.1 + - + +
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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
----------------------------------------------------------
195A ALA* 3.6 12.2 + - + +
199A GLY* 3.5 23.5 - - - -
200A VAL* 3.2 45.5 + - + +
202A GLN* 5.9 1.8 - - - -
211A THR* 4.6 12.6 + - - -
214A GLN* 3.1 36.3 + - - +
65B GLY 3.4 14.0 + - - +
66B TYR* 3.4 8.0 + - + +
67B ALA 3.4 0.4 - - - -
68B ILE* 1.4 78.8 - - + +
70B LEU* 1.4 66.3 + - + +
72B HIS* 3.3 19.2 + - + +
73B ILE* 3.6 19.2 + - + +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 5.3 13.7 - - + -
66B TYR* 3.2 66.3 + - + +
67B ALA* 4.2 6.3 - - - +
68B ILE 3.4 0.4 - - - -
69B LYS* 1.4 76.3 - - + +
71B ILE* 1.4 58.0 + - + +
72B HIS 3.4 0.2 - - - -
73B ILE* 4.5 5.2 - - + +
74B PRO* 3.1 20.8 - - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 6.4 0.2 - - + -
47A GLN* 3.4 41.1 - - + +
67B ALA 3.4 17.9 + - - +
68B ILE* 3.5 6.1 - - - +
70B LEU* 1.4 75.9 - - + +
72B HIS* 1.4 64.4 + - - +
73B ILE 3.4 1.1 - - - -
74B PRO* 3.6 18.9 - - + +
75B ILE* 3.5 17.0 + - + +
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Residues in contact with HIS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 5.5 0.7 - - - -
47A GLN* 3.7 29.5 + - - -
75A GLU* 6.2 0.4 - - - -
68B ILE* 3.2 22.1 + - + +
69B LYS* 3.3 13.4 + - + +
71B ILE* 1.4 75.8 - - - +
73B ILE* 1.4 67.2 + - + +
75B ILE* 3.2 30.5 + - + +
76B ARG* 3.9 5.4 + - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 3.9 28.7 - - + -
202A GLN* 3.7 37.9 - - + +
69B LYS* 3.6 18.4 + - + +
70B LEU* 4.5 3.6 - - + +
72B HIS* 1.4 78.9 - - + +
74B PRO* 1.3 69.1 - - + +
76B ARG* 3.2 18.4 + - + +
77B TYR* 3.4 10.8 + - + +
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Residues in contact with PRO 74 (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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70B LEU 3.1 26.0 - - - +
71B ILE* 3.6 17.7 - - + +
73B ILE* 1.3 86.9 - - + +
75B ILE* 1.4 61.3 + - - +
76B ARG 3.3 0.2 - - - -
77B TYR* 3.6 13.2 - - + +
78B VAL* 3.1 32.8 + - + +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.2 43.1 - - - +
48A PHE* 4.9 2.5 - - - -
49A PRO* 5.0 15.7 - - + -
71B ILE* 3.5 9.4 - - + +
72B HIS* 3.2 30.8 + - + +
74B PRO* 1.4 75.7 - - - +
76B ARG* 1.4 63.3 + - + +
78B VAL* 3.6 2.2 + - - +
79B ILE* 3.1 41.0 + - + +
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Residues in contact with ARG 76 (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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56A ALA 4.2 18.7 + - - -
57A THR* 4.9 7.9 + - - +
60A ASN* 4.7 15.1 + - - +
204A LYS* 5.1 19.7 - - + +
72B HIS* 3.9 4.6 + - + +
73B ILE* 3.2 11.2 + - + +
75B ILE* 1.4 79.1 + - + +
77B TYR* 1.4 61.8 + - - +
79B ILE* 2.9 42.2 + - - +
80B VAL* 3.3 34.0 + - - +
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.4 7.6 + - + +
74B PRO* 3.6 20.4 - - + +
75B ILE 3.3 0.2 - - - -
76B ARG* 1.4 78.1 - - - +
78B VAL* 1.4 77.0 + - + +
79B ILE 4.5 1.4 - - - -
80B VAL* 4.8 2.1 + - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PRO* 3.1 19.6 + - + +
75B ILE* 4.1 3.4 - - - +
77B TYR* 1.4 90.8 - - + +
79B ILE* 1.4 69.2 + - + +
80B VAL 4.1 1.6 + - - -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.1 21.8 + - + +
76B ARG* 2.9 42.8 + - - +
78B VAL* 1.4 87.4 - - + +
80B VAL* 1.4 69.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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