Contacts of the helix formed by residues 72 - 85 (chain B) in PDB entry 1XAI
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 THR 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B GLU 4.9 3.6 - - - +
69B LYS* 4.2 19.4 + - - +
70B THR 2.8 7.8 + - - +
71B LYS* 1.3 80.1 - - - +
73B PHE* 1.3 63.8 + - - +
74B GLU* 3.4 15.8 + - - +
75B GLN* 3.2 21.5 + - - +
76B TYR* 3.2 20.4 + - - +
139B ILE* 3.9 8.5 - - - +
140B ASN* 4.6 4.7 - - + -
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Residues in contact with PHE 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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76A TYR* 3.8 18.6 - + - -
77A GLN* 3.4 51.1 - - + +
80A LEU* 3.6 41.7 - - + -
81A GLU* 3.6 33.0 - - + -
72B THR* 1.3 73.4 - - - +
74B GLU* 1.3 67.0 + - - +
76B TYR* 3.0 23.9 + + - +
77B GLN* 3.2 9.0 + - - +
139B ILE* 4.0 14.1 - - + +
140B ASN 4.3 10.3 + - - -
148B ILE* 3.7 22.4 - - + -
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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
----------------------------------------------------------
77A GLN* 3.4 25.7 - - - +
72B THR* 3.4 14.0 + - - +
73B PHE* 1.3 85.1 + - - +
75B GLN* 1.3 62.0 + - - +
77B GLN* 3.4 8.5 + - - +
78B GLU* 3.3 20.9 + - - +
142B LYS* 6.1 0.7 - - - -
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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
----------------------------------------------------------
63B ILE 5.5 1.2 + - - -
64B ILE* 4.6 4.6 - - - +
65B PRO* 3.0 32.6 - - + +
69B LYS 5.2 0.7 - - - +
70B THR* 3.3 40.6 - - - +
72B THR* 3.2 10.3 + - - +
74B GLU* 1.3 76.9 - - - +
76B TYR* 1.3 67.5 + - - +
78B GLU* 3.3 32.5 + - - +
79B THR* 2.6 55.6 + - - -
105B PHE* 3.6 7.4 - - + -
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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
----------------------------------------------------------
73A PHE* 3.9 24.0 - + - -
76A TYR* 4.1 25.1 - + - -
108A PHE* 3.4 11.3 - + - -
148A ILE* 3.6 2.1 - - - +
72B THR 3.2 12.9 + - - +
73B PHE* 3.0 16.1 + + - +
75B GLN* 1.3 77.8 - - - +
77B GLN* 1.3 62.3 + - - +
79B THR* 4.2 1.0 - - - -
80B LEU* 3.2 38.6 + - + +
105B PHE* 3.7 13.1 - + + -
108B PHE* 3.4 41.4 - + - -
109B VAL* 4.2 13.0 - - + -
112B THR* 2.6 41.8 + - - +
139B ILE* 4.4 6.5 - - + -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.4 54.8 - - + +
74A GLU* 3.6 27.1 + - - +
77A GLN* 5.9 2.8 - - - +
142A LYS* 4.3 15.7 + - - +
73B PHE 3.2 6.8 + - - +
74B GLU* 3.8 10.5 + - - +
75B GLN 3.3 0.2 - - - -
76B TYR* 1.3 76.8 - - - +
78B GLU* 1.3 70.0 + - - +
80B LEU* 3.1 2.6 + - - +
81B GLU* 2.8 34.0 + - + +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 5.8 0.3 - - - +
74B GLU 3.3 10.3 + - - +
75B GLN* 3.3 32.1 + - - +
77B GLN* 1.3 80.2 - - - +
79B THR* 1.3 54.9 + - - +
81B GLU* 3.3 4.7 + - - +
82B TYR* 2.7 41.7 + - + +
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Residues in contact with THR 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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37B LEU* 4.5 12.3 - - + -
62B VAL* 4.2 22.7 - - + +
64B ILE* 4.0 3.5 - - - +
75B GLN* 2.6 39.7 + - - +
76B TYR 4.2 0.9 - - - -
78B GLU* 1.3 78.2 - - - +
80B LEU* 1.3 57.8 + - - +
82B TYR* 3.6 5.5 - - - +
83B ILE* 2.9 37.3 + - + +
105B PHE* 3.5 24.6 - - + -
109B VAL* 4.5 6.7 - - + -
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Residues in contact with LEU 80 (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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73A PHE* 3.7 26.2 - - + -
148A ILE* 3.7 17.9 - - + -
76B TYR* 3.2 48.8 + - + +
77B GLN 3.1 4.0 + - - +
79B THR* 1.3 74.5 - - - +
81B GLU* 1.3 63.2 + - - +
83B ILE* 3.0 6.0 + - + +
84B LEU* 2.8 34.2 + - + +
109B VAL* 3.6 34.1 - - + +
112B THR* 4.0 1.1 - - - +
113B LEU* 3.6 31.2 - - + -
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Residues in contact with GLU 81 (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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73A PHE* 3.7 28.4 - - + -
141A SER* 2.6 30.6 + - - -
142A LYS* 3.2 49.0 + - + +
143A GLN* 4.8 3.3 - - - +
77B GLN* 2.8 32.4 + - + +
78B GLU* 3.7 4.5 - - - +
80B LEU* 1.3 72.8 - - - +
82B TYR* 1.3 65.8 + - - +
84B LEU* 3.4 4.9 + - - +
85B SER* 3.1 22.2 + - - -
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Residues in contact with TYR 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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35B PHE* 5.2 1.3 - + - -
60B HIS* 6.2 1.6 - - + -
61B LYS 5.0 6.8 + - - -
62B VAL* 4.4 18.8 - - + -
78B GLU* 2.7 26.6 + - + +
79B THR* 3.6 8.3 - - - +
81B GLU* 1.3 72.9 - - - +
83B ILE* 1.3 78.4 + - + +
85B SER* 2.4 28.1 + - - -
86B HIS* 3.0 35.7 + + - -
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Residues in contact with ILE 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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35B PHE* 3.6 35.9 - - + -
37B LEU* 5.0 1.6 - - + -
62B VAL* 3.6 25.8 - - + -
79B THR* 2.9 27.4 + - + +
80B LEU* 3.0 10.7 + - - +
82B TYR* 1.3 81.9 - - + +
84B LEU* 1.3 62.0 + - - +
86B HIS* 2.8 32.5 + - - +
88B VAL* 3.8 20.0 - - + +
94B ILE* 5.0 8.3 - - + -
109B VAL* 5.1 4.9 - - + -
113B LEU* 4.0 24.7 - - + -
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Residues in contact with LEU 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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141A SER* 3.4 33.7 - - - +
143A GLN* 3.9 16.8 - - + +
147A LEU* 3.6 12.1 - - + +
148A ILE* 3.6 20.6 - - + -
312A SER* 5.1 0.9 + - - -
80B LEU 2.8 23.0 + - - +
81B GLU* 3.9 6.5 - - - +
83B ILE* 1.3 69.8 - - - +
85B SER* 1.3 52.7 + - - +
86B HIS 2.5 18.6 + - - -
87B HIS* 2.8 18.9 + - - -
88B VAL* 4.0 11.9 + - + -
113B LEU* 3.6 26.5 - - + -
114B LEU* 3.9 23.1 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 2.9 24.6 + - - -
81B GLU 3.1 10.6 + - - -
82B TYR* 2.4 29.0 + - - -
83B ILE 3.0 1.4 + - - -
84B LEU* 1.3 73.0 - - - +
86B HIS* 1.3 64.5 + - - +
87B HIS* 3.5 10.7 + - - -
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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