Contacts of the helix formed by residues 72 - 85 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLU 4.9 3.6 - - - +
69A LYS* 4.2 18.8 + - - +
70A THR 2.8 7.9 + - - +
71A LYS* 1.3 80.8 - - - +
73A PHE* 1.3 63.5 + - - +
74A GLU* 3.4 15.5 + - - +
75A GLN* 3.2 22.9 + - - +
76A TYR* 3.2 20.1 + - - +
139A ILE* 3.9 8.3 - - - +
140A ASN* 4.6 5.2 - - + +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 1.3 70.5 - - - +
74A GLU* 1.3 70.9 + - - +
76A TYR* 3.0 21.7 + + - +
77A GLN* 3.2 8.7 + - - +
139A ILE* 3.9 17.6 - - + +
140A ASN 4.3 10.5 + - - -
148A ILE* 3.7 24.5 - - + -
76B TYR* 3.9 17.7 - + - -
77B GLN* 3.4 51.1 - - + +
80B LEU* 3.7 39.7 - - + -
81B GLU* 3.7 31.9 - - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 3.4 13.7 - - - +
73A PHE* 1.3 85.5 + - - +
75A GLN* 1.3 62.0 + - - +
77A GLN* 3.4 9.0 + - - +
78A GLU* 3.3 20.2 + - - +
142A LYS* 6.2 0.2 - - - -
77B GLN* 3.6 27.1 + - - +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE 5.6 0.8 + - - -
64A ILE* 4.7 3.4 - - - +
65A PRO* 3.0 31.5 - - + +
69A LYS 5.2 0.7 - - - +
70A THR* 3.3 38.8 - - - +
72A THR* 3.2 11.4 + - - +
74A GLU* 1.3 77.2 - - - +
76A TYR* 1.3 66.6 + - - +
78A GLU* 3.2 32.8 + - - +
79A THR* 2.6 49.1 + - - -
105A PHE* 3.5 9.2 - - + -
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR 3.2 14.2 + - - +
73A PHE* 3.0 18.3 + + - +
75A GLN* 1.3 76.3 - - - +
77A GLN* 1.3 62.3 + - - +
79A THR* 4.2 1.0 - - - -
80A LEU* 3.2 36.5 + - + +
105A PHE* 3.7 13.1 - + + -
108A PHE* 3.4 42.3 - + - -
109A VAL* 4.2 12.9 - - + +
112A THR* 2.5 41.1 + - - +
139A ILE* 4.4 5.2 - - + -
73B PHE* 3.8 23.6 - + - -
76B TYR* 4.1 25.6 - + - -
108B PHE* 3.5 5.7 - + - -
148B ILE* 3.5 9.3 - - + +
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Residues in contact with GLN 77 (chain A).
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 3.2 7.8 + - - +
74A GLU* 3.8 9.8 + - - +
75A GLN 3.3 0.2 - - - -
76A TYR* 1.3 76.6 - - - +
78A GLU* 1.3 69.8 + - - +
80A LEU* 3.1 2.6 + - - +
81A GLU* 2.8 33.9 + - + +
73B PHE* 3.4 55.6 - - + +
74B GLU* 3.4 27.9 + - - +
77B GLN* 5.9 2.6 - - - +
142B LYS* 4.2 15.0 + - - +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE 5.7 0.9 - - - +
74A GLU 3.3 11.0 + - - +
75A GLN* 3.2 31.2 + - - +
77A GLN* 1.3 81.2 - - - +
79A THR* 1.3 53.8 + - - +
81A GLU* 3.6 4.3 - - - +
82A TYR* 2.7 42.3 + - + +
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.3 13.0 - - + -
62A VAL* 4.3 15.2 - - + +
64A ILE* 4.0 4.6 - - + +
75A GLN* 2.6 37.7 + - - +
76A TYR 4.2 0.9 - - - -
78A GLU* 1.3 78.0 - - - +
80A LEU* 1.3 58.8 + - - +
82A TYR* 3.6 6.0 - - - +
83A ILE* 2.9 43.4 + - + +
105A PHE* 3.6 25.4 - - + -
109A VAL* 4.5 7.6 - - + -
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Residues in contact with LEU 80 (chain A).
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* 3.2 47.4 + - + +
77A GLN 3.1 4.7 + - - +
79A THR* 1.3 74.7 - - - +
81A GLU* 1.3 61.8 + - - +
83A ILE* 3.0 6.0 + - + +
84A LEU* 2.8 34.8 + - + +
109A VAL* 3.6 33.9 - - + +
112A THR* 4.0 0.9 - - - +
113A LEU* 3.6 30.1 - - + -
73B PHE* 3.6 25.6 - - + -
148B ILE* 3.6 20.0 - - + -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLN* 2.8 32.7 + - + +
78A GLU* 3.7 4.0 - - - +
80A LEU* 1.3 73.3 - - - +
82A TYR* 1.3 65.2 + - - +
84A LEU* 3.9 3.7 - - - +
85A SER* 3.1 21.8 + - - -
73B PHE* 3.6 27.8 - - + -
141B SER* 2.6 30.4 + - - -
142B LYS* 3.2 48.3 + - + +
143B GLN* 4.7 3.3 - - - +
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.3 0.7 - + - -
60A HIS* 6.2 1.6 - - + -
61A LYS 5.2 5.0 + - - -
62A VAL* 4.6 17.3 - - + -
78A GLU* 2.7 28.1 + - + +
79A THR* 3.6 6.7 - - - +
81A GLU* 1.3 72.9 - - - +
83A ILE* 1.3 77.8 + - + +
85A SER* 2.5 28.3 + - - -
86A HIS* 3.0 36.5 + + - -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.7 27.1 - - + -
37A LEU* 5.0 2.2 - - + -
62A VAL* 3.7 30.5 - - + -
79A THR* 2.9 32.1 + - + +
80A LEU* 3.0 10.7 + - + +
82A TYR* 1.3 84.8 - - + +
84A LEU* 1.3 65.0 + - - +
86A HIS* 2.9 27.6 + - - +
88A VAL* 3.8 19.2 - - + +
94A ILE* 5.0 7.6 - - + -
109A VAL* 5.2 4.0 - - + -
113A LEU* 3.9 26.2 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 2.8 22.0 + - - +
81A GLU* 3.9 5.2 - - - +
83A ILE* 1.3 69.4 - - - +
85A SER* 1.3 52.0 + - - +
86A HIS 2.5 17.8 + - - -
87A HIS* 2.8 19.8 + - - -
88A VAL* 4.0 11.3 + - + -
113A LEU* 3.7 24.9 - - + -
114A LEU* 3.8 23.8 - - + -
141B SER* 3.3 34.3 - - - +
143B GLN* 3.9 18.6 - - + +
147B LEU* 3.6 12.6 - - + +
148B ILE* 3.5 21.8 - - + -
312B SER* 5.1 1.0 + - - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU 3.1 11.6 + - - -
82A TYR* 2.5 25.7 + - - -
83A ILE 3.0 1.0 + - - -
84A LEU* 1.3 73.0 - - - +
86A HIS* 1.3 64.4 + - - +
87A HIS* 3.5 8.5 + - - -
143B GLN* 2.9 24.6 + - - -
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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
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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