Contacts of the helix formed by residues 71 - 89 (chain B) in PDB entry 2XWU
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 VAL 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 5.6 0.9 - - + +
35B TYR* 4.0 10.5 - - - +
69B ASP 3.5 5.3 + - - +
70B LYS* 1.3 74.6 - - - +
72B PRO* 1.4 75.4 - - + +
73B GLU* 3.3 19.5 - - - +
74B ILE* 3.0 34.8 + - + +
75B GLN* 2.9 17.7 + - - +
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Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS 3.9 1.1 - - - +
71B VAL* 1.4 86.7 - - + +
73B GLU* 1.3 77.3 + - - +
75B GLN* 2.9 20.1 + - - +
76B TYR* 2.8 22.0 + - - +
116B SER* 4.0 26.7 - - - +
118B ILE* 4.3 8.7 - - + -
119B VAL* 3.9 2.4 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.1 19.5 - - + -
137A TYR* 6.6 0.2 - - + -
138A CYS* 5.3 20.7 - - + +
141A ARG* 4.8 14.6 + - - +
34B TYR* 3.3 39.2 + - + -
35B TYR* 3.8 9.0 + - - +
71B VAL* 3.3 22.2 - - - +
72B PRO* 1.3 87.3 - - + +
74B ILE* 1.3 61.4 + - - +
76B TYR* 3.2 19.1 - - - +
77B PHE 3.4 2.1 + - - -
118B ILE* 4.4 4.8 - - + +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.9 17.5 - - + +
30B LEU* 3.5 27.9 - - + +
31B HIS* 3.3 35.2 - - + +
34B TYR* 4.2 8.7 - - + -
35B TYR* 5.1 1.1 - - + +
65B LEU* 3.3 30.9 - - + +
70B LYS* 4.1 10.3 - - + -
71B VAL* 3.0 34.8 + - + +
73B GLU* 1.3 76.4 - - - +
75B GLN* 1.3 63.7 + - - +
77B PHE* 3.3 13.0 + - - +
78B GLY 3.6 6.4 + - - -
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Residues in contact with GLN 75 (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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65B LEU 3.2 21.3 - - - +
66B LEU* 3.5 15.3 + - + +
67B GLN 3.2 15.4 + - - +
68B PRO* 4.0 11.1 + - - +
70B LYS* 2.7 23.6 + - + +
71B VAL 2.9 15.7 + - - +
72B PRO* 2.9 21.0 + - - +
74B ILE* 1.3 72.7 - - - +
76B TYR* 1.3 66.0 + - - +
78B GLY* 3.0 12.3 + - - -
79B ALA* 3.0 10.4 + - - +
111B ARG* 5.6 0.2 - - - +
112B PHE* 3.3 26.1 - - - -
116B SER* 4.4 4.9 + - - -
119B VAL* 3.7 12.8 - - + +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN* 4.5 11.3 + - - -
125A ILE* 3.7 29.4 - - + -
126A GLN* 4.8 14.9 - - + +
34B TYR* 5.0 1.6 - - - -
72B PRO 2.8 10.8 + - - +
73B GLU 3.2 11.2 - - - +
75B GLN* 1.3 77.7 - - - +
77B PHE* 1.3 53.2 + - - +
79B ALA* 3.0 4.1 + - - +
80B SER* 2.6 48.9 + - - -
118B ILE* 3.6 50.7 - - + -
119B VAL* 3.7 6.7 - - - +
122B ARG* 2.9 45.7 + - + -
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Residues in contact with PHE 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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26B VAL* 3.5 25.6 - - + -
30B LEU* 3.7 26.9 - - + -
34B TYR* 4.6 3.1 - - - +
49B LEU* 3.7 40.8 - - + -
52B ALA* 4.8 0.4 - - + -
53B GLN* 4.0 28.0 - - + -
61B PHE* 3.7 15.7 - + - -
65B LEU* 3.6 16.6 - - + -
73B GLU 3.4 3.9 + - - +
74B ILE 3.3 10.9 + - - +
75B GLN 3.2 0.8 - - - -
76B TYR* 1.3 81.9 - - - +
78B GLY* 1.3 58.7 + - - +
80B SER* 3.7 7.4 - - - -
81B ALA* 2.7 35.2 + - + +
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Residues in contact with GLY 78 (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 SER* 3.3 35.8 - - - -
65B LEU* 3.8 18.0 - - - +
66B LEU* 4.5 1.6 - - - -
74B ILE 3.6 4.2 + - - -
75B GLN 3.0 8.4 + - - -
77B PHE* 1.3 80.4 - - - +
79B ALA* 1.3 61.8 + - - +
81B ALA* 3.2 0.8 + - - -
82B LEU* 3.0 19.6 + - - +
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Residues in contact with ALA 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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66B LEU* 3.9 3.6 - - + +
75B GLN 3.0 5.5 + - - +
76B TYR* 3.0 5.9 + - - +
78B GLY* 1.3 74.9 - - - +
80B SER* 1.3 63.4 + - - +
82B LEU* 3.3 5.9 + - - +
83B HIS* 3.2 17.5 + - - +
119B VAL* 3.9 17.5 - - + -
122B ARG* 3.4 28.2 - - + +
123B LEU* 3.8 34.4 - - + +
126B ALA* 4.8 0.5 - - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 2.6 33.0 + - - -
77B PHE* 3.7 10.1 - - - -
79B ALA* 1.3 72.4 - - - +
81B ALA* 1.3 65.2 + - - +
83B HIS* 3.1 5.2 + - - +
84B ILE* 3.0 36.8 + - - +
122B ARG* 3.3 31.4 + - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLN* 4.1 24.0 - - + +
58B ALA* 4.6 6.1 - - + -
61B PHE* 4.8 2.7 - - + -
62B SER* 4.1 12.8 - - - -
77B PHE* 2.7 31.3 + - + +
78B GLY* 3.7 4.7 - - - +
80B SER* 1.3 73.5 - - - +
82B LEU* 1.3 61.8 + - - +
84B ILE* 3.3 11.5 + - - +
85B LYS* 3.1 28.5 + - - +
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Residues in contact with LEU 82 (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 ALA 5.0 0.9 - - - +
59B TRP* 4.9 16.6 - - + -
62B SER* 3.2 27.3 - - - +
63B TRP* 3.7 57.0 - - + +
66B LEU* 4.4 6.5 - - + -
78B GLY 3.0 8.0 + - - +
79B ALA 3.5 8.1 - - - +
80B SER 3.1 0.2 - - - -
81B ALA* 1.3 76.2 - - - +
83B HIS* 1.3 64.2 + - - +
85B LYS* 3.5 5.4 + - + +
86B ILE* 3.1 31.7 + - + +
105B LEU* 4.0 13.5 - - + -
123B LEU* 4.0 16.2 - - + -
126B ALA* 4.5 8.3 - - + -
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Residues in contact with HIS 83 (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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79B ALA 3.2 8.9 + - - +
80B SER 3.1 10.6 + - - +
82B LEU* 1.3 80.8 - - - +
84B ILE* 1.3 62.9 + - + +
86B ILE* 3.3 1.2 + - - -
87B SER* 2.8 53.0 + - - -
122B ARG* 3.8 23.0 + - - -
125B VAL* 3.2 44.6 - - + +
126B ALA* 3.8 18.6 - - + +
129B SER* 4.1 4.0 - - - -
176B GLU* 3.5 22.5 + - - -
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Residues in contact with ILE 84 (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* 3.6 42.0 - - - +
54B VAL* 4.1 17.5 - - + -
80B SER* 3.0 43.3 + - - +
81B ALA* 3.6 8.5 - - - +
82B LEU 3.2 0.2 - - - -
83B HIS* 1.3 83.0 - - + +
85B LYS* 1.3 60.3 + - + +
87B SER* 3.5 6.1 - - - +
88B ARG* 2.5 69.1 + - + +
89B TYR* 4.6 0.2 - - + -
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Residues in contact with LYS 85 (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 3.3 20.2 - - - +
54B VAL 2.6 18.0 + - - +
55B SER 2.6 29.6 + - - +
56B PRO* 3.9 2.8 - - - +
58B ALA* 3.7 13.7 - - + -
59B TRP* 2.9 58.0 - - + +
81B ALA 3.1 17.5 + - - +
82B LEU* 3.9 5.8 - - + +
83B HIS 3.4 0.2 - - - -
84B ILE* 1.3 75.5 - - + +
86B ILE* 1.3 57.3 + - - +
89B TYR* 2.7 55.5 + - + +
92B ASP* 4.1 3.8 + - - -
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Residues in contact with ILE 86 (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 TRP* 4.1 19.7 - - + -
82B LEU* 3.1 22.8 + - + +
83B HIS 4.1 1.6 - - - +
85B LYS* 1.3 77.7 - - - +
87B SER* 1.3 64.7 + - - +
89B TYR 4.7 0.2 - - - -
90B TRP* 3.4 50.7 - - + +
93B ILE* 4.6 0.4 - - + -
101B LEU* 4.2 20.0 - - + -
105B LEU* 4.0 29.4 - - + -
126B ALA* 4.0 12.3 - - + +
129B SER* 4.2 4.9 + - - +
130B LEU* 3.8 20.0 - - + +
133B SER* 4.8 2.1 + - - -
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Residues in contact with SER 87 (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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83B HIS* 2.8 39.2 + - - -
84B ILE* 3.1 9.5 + - - +
86B ILE* 1.3 78.7 - - - +
88B ARG* 1.3 74.0 + - - +
90B TRP* 5.2 1.9 + - - +
129B SER* 3.3 21.5 + - - -
176B GLU* 4.7 2.7 - - - -
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Residues in contact with ARG 88 (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* 5.2 5.7 - - - +
54B VAL* 4.4 12.3 - - - +
84B ILE* 2.5 50.8 + - + +
87B SER* 1.3 85.1 + - - +
89B TYR* 1.3 80.5 + - + +
90B TRP 3.6 3.3 + - - -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.7 45.0 + - + +
59B TRP* 3.1 20.0 - - + -
84B ILE* 4.6 0.4 - - + -
85B LYS* 2.7 44.1 + - + +
88B ARG* 1.3 93.9 + - + +
90B TRP* 1.3 62.7 + - - +
91B SER* 3.1 4.0 - - - +
92B ASP* 3.3 33.0 + - - +
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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
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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