Contacts of the helix formed by residues 63 - 79 (chain B) in PDB entry 5WWT
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 SER 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASN* 2.7 21.8 + - - -
232A PRO 4.7 6.1 - - - -
233A GLN* 2.5 36.0 + - - -
234A PRO* 4.8 2.3 - - - +
57B VAL* 3.9 1.3 - - - -
59B THR* 5.2 4.7 - - - +
62B ALA* 1.3 76.1 - - - +
64B VAL* 1.3 63.4 + - - +
65B GLN 3.8 1.5 + - - -
66B HIS 3.3 10.0 + - - -
67B VAL* 3.1 24.1 + - - +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLN* 5.2 5.4 - - - +
57B VAL* 3.9 19.5 - - + +
59B THR* 4.4 10.7 - - + +
63B SER* 1.3 74.7 - - - +
65B GLN* 1.3 58.4 + - - +
67B VAL* 3.9 1.2 - - - +
68B LYS* 2.9 28.4 + - + +
88B GLN* 3.6 33.9 - - + +
93B GLN 3.6 19.5 - - - +
94B ASP* 3.9 14.6 - - - -
96B LEU* 3.7 24.4 - - + +
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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
----------------------------------------------------------
228A HIS 3.7 3.3 - - - +
229A VAL 4.8 4.4 + - - -
231A ASN* 3.5 39.8 - - - +
398A PRO 5.5 1.2 + - - -
399A GLN* 5.0 0.6 - - - +
400A GLU* 3.2 58.5 + - + +
462A LYS* 5.2 9.3 - - - +
63B SER* 3.2 0.8 + - - -
64B VAL* 1.3 77.3 - - - +
66B HIS* 1.3 64.2 + - - +
68B LYS* 3.1 9.8 + - - +
69B ASN* 3.0 39.7 + - - +
88B GLN* 5.9 0.9 - - - -
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Residues in contact with HIS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 3.8 5.3 + - - +
233A GLN* 3.4 32.6 - - + +
319A ARG* 6.0 2.0 + - - -
62B ALA* 4.3 11.7 - - + -
63B SER* 3.3 18.1 + - - +
65B GLN* 1.3 79.3 - - - +
67B VAL* 1.3 61.9 + - - +
69B ASN* 3.1 13.8 + - - +
70B LEU* 3.0 58.9 + - + +
215B TYR* 4.5 10.0 + + - -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 3.7 30.7 - - + -
62B ALA* 3.7 20.2 - - + -
63B SER 3.1 17.8 + - - +
64B VAL 3.9 2.9 - - - +
66B HIS* 1.3 78.5 - - - +
68B LYS* 1.3 57.8 + - - +
70B LEU* 3.3 8.3 + - - +
71B LEU* 2.9 30.4 + - + +
96B LEU* 4.1 5.6 - - + -
212B LEU* 4.6 2.7 - - + -
215B TYR* 3.7 18.8 - - + -
216B LEU* 3.5 30.5 - - + -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLU* 3.5 34.3 + - - +
64B VAL 2.9 20.9 + - - +
65B GLN* 3.1 8.9 + - - +
67B VAL* 1.3 76.8 - - - +
69B ASN* 1.3 59.2 + - - +
71B LEU* 3.4 4.2 + - - +
72B LEU* 2.9 48.1 + - + +
86B ILE* 3.5 39.2 + - + +
88B GLN* 5.6 8.4 - - + +
96B LEU* 3.9 19.7 - - + +
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 5.5 0.8 - - - +
400A GLU* 4.3 12.0 + - - +
65B GLN* 3.0 38.4 + - - +
66B HIS* 3.1 11.7 + - - +
68B LYS* 1.3 76.6 - - - +
70B LEU* 1.3 67.8 + - + +
72B LEU* 3.0 20.5 + - - +
73B ASP* 3.0 27.9 + - - +
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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
----------------------------------------------------------
66B HIS* 3.0 51.8 + - + +
67B VAL* 3.7 7.2 - - - +
69B ASN* 1.3 78.5 - - + +
71B LEU* 1.3 58.0 + - - +
73B ASP* 3.3 15.3 + - - +
74B GLU* 2.9 25.5 + - - +
212B LEU* 3.7 34.4 - - + +
215B TYR* 4.0 18.4 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.8 7.4 - - + -
67B VAL 2.9 17.0 + - - +
68B LYS 3.8 4.0 - - - +
70B LEU* 1.3 74.8 - - - +
72B LEU* 1.3 60.8 + - - +
74B GLU* 3.6 6.8 - - + +
75B LEU* 2.9 37.1 + - + +
86B ILE* 3.8 11.9 - - + -
96B LEU* 4.1 22.0 - - + -
98B ILE* 4.9 7.6 - - + -
208B PHE* 4.1 23.3 - - + -
211B VAL* 4.1 11.2 - - + -
212B LEU* 3.8 13.0 - - + -
216B LEU* 3.7 40.2 - - + -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 2.9 38.7 + - + +
69B ASN* 3.0 24.4 + - - +
71B LEU* 1.3 77.9 - - - +
73B ASP* 1.3 59.7 + - - +
75B LEU* 3.5 4.7 + - + +
76B GLN* 2.9 27.7 + - - +
84B VAL 4.8 9.0 - - - +
85B PRO* 5.6 0.7 - - + -
86B ILE* 3.7 28.7 - - + +
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Residues in contact with ASP 73 (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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69B ASN* 3.0 17.9 + - - +
70B LEU* 3.5 18.6 - - + +
72B LEU* 1.3 77.6 - - - +
74B GLU* 1.3 61.9 + - - +
76B GLN* 3.1 10.7 + - - +
77B LYS* 3.0 39.2 + - - +
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Residues in contact with GLU 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 2.9 16.9 + - - +
71B LEU* 3.6 16.2 - - + +
72B LEU 3.3 0.2 - - - -
73B ASP* 1.3 76.8 - - - +
75B LEU* 1.3 59.8 + - + +
77B LYS* 3.1 25.2 + - - +
78B GLN* 2.9 60.9 + - - +
211B VAL* 3.7 31.3 - - + +
212B LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 2.9 23.9 + - + +
72B LEU* 3.9 6.3 - - + +
74B GLU* 1.3 81.4 - - + +
76B GLN* 1.3 64.8 + - - +
78B GLN* 4.5 5.2 - - - +
79B PHE* 3.1 38.1 + - + +
81B GLY 4.9 0.3 + - - -
82B LEU 5.2 2.3 + - - +
84B VAL* 3.6 30.3 - - + +
86B ILE* 4.0 13.9 - - + -
98B ILE* 3.9 30.5 - - + -
206B PRO* 3.5 31.9 - - + -
208B PHE* 5.5 2.2 - - + -
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU 2.9 15.1 + - - +
73B ASP* 3.1 17.0 + - - +
75B LEU* 1.3 77.4 - - - +
77B LYS* 1.3 59.7 + - + +
80B ASN* 3.9 1.2 - - - -
81B GLY* 3.1 52.1 + - - +
82B LEU 4.0 7.2 - - - +
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Residues in contact with LYS 77 (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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73B ASP* 3.0 30.7 + - - +
74B GLU* 3.1 26.3 + - - +
76B GLN* 1.3 77.4 - - + +
78B GLN* 1.3 65.8 + - + +
80B ASN* 3.4 11.6 + - - -
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU* 2.9 53.3 + - - +
75B LEU* 4.4 5.1 - - - +
77B LYS* 1.3 76.0 - - + +
79B PHE* 1.3 71.0 + - + +
80B ASN* 3.2 6.1 + - - +
129B HIS* 5.6 0.3 + - - -
206B PRO* 3.5 14.5 - - - +
207B SER* 3.0 49.4 + - - +
211B VAL* 4.9 1.2 - - - +
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Residues in contact with PHE 79 (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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75B LEU* 3.1 23.9 + - + +
78B GLN* 1.3 85.9 - - + +
80B ASN* 1.3 69.6 - - - +
81B GLY 3.1 3.0 + - - -
82B LEU* 3.1 42.0 + - + +
84B VAL* 3.6 35.7 - - + -
98B ILE* 5.4 0.7 - - + -
99B PRO 6.1 0.4 - - - -
101B ILE* 5.9 0.4 - - + -
204B LEU* 3.7 37.5 - - + -
205B SER* 3.9 5.2 - - - -
206B PRO* 3.6 46.0 - - + -
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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