Contacts of the helix formed by residues 62 - 77 (chain B) in PDB entry 1XI1
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 ASN 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 4.6 0.7 - - - -
61B HIS* 1.3 78.6 - - - +
63B LEU* 1.3 63.4 + - - +
64B LYS* 3.2 13.2 - - - +
65B PHE* 3.1 25.1 + - - +
66B ALA* 3.8 4.2 + - - +
121B ASP* 2.6 18.4 + - - +
123B LEU* 3.5 28.1 - - + +
3D T 4.1 17.7 + - - +
4D T 3.1 50.7 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.8 17.9 + - + +
61B HIS 3.8 0.4 - - - -
62B ASN* 1.3 67.2 - - - +
64B LYS* 1.3 56.4 + - - +
65B PHE 2.9 6.3 - - - -
66B ALA 4.5 0.2 - - - +
67B GLY* 2.6 52.2 + - - +
70B ILE* 5.1 0.2 - - + -
100B TRP* 3.9 17.1 - - + -
101B TYR 4.1 2.7 - - - -
102B MET* 4.0 24.0 - - - +
103B ILE* 4.1 10.3 - - + -
119B ILE* 3.7 32.3 - - + +
120B TYR 3.8 20.2 - - - +
121B ASP* 2.8 29.7 + - + +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 3.2 13.0 - - - +
63B LEU* 1.3 76.7 - - - +
65B PHE* 1.3 59.9 + - - +
68B ALA* 4.2 6.6 + - - +
97B MET 4.8 2.6 + - - -
98B GLY* 2.9 33.7 + - - +
99B GLN* 5.3 1.3 - - - -
100B TRP* 3.4 50.2 + - + +
121B ASP* 5.1 1.0 + - - +
402B LYS* 5.7 1.4 - - - +
558B PRO* 5.1 17.9 - - - -
560B GLN* 5.3 1.4 + - - -
565B VAL* 4.6 4.2 - - - +
3D T 5.1 11.2 - - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 5.5 4.9 - - + -
15B THR* 3.4 30.1 - - + -
62B ASN* 3.1 24.0 + - - +
63B LEU 2.9 1.2 + - - -
64B LYS* 1.3 77.4 - - - +
66B ALA* 1.3 71.8 + - + +
67B GLY 3.2 1.1 - - - -
68B ALA* 3.1 15.9 + - - +
69B PHE* 3.5 26.5 - + - -
558B PRO* 6.0 0.2 - - + -
565B VAL* 3.8 39.5 - - + -
566B VAL* 5.1 0.7 - - - -
567B LEU* 4.5 16.2 - - + -
4D T 4.2 26.0 - - + +
5D T 3.7 29.4 - - - -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.8 16.1 - - + +
60B PHE* 3.3 49.1 - - + -
61B HIS 6.1 0.2 - - - +
62B ASN 3.8 4.3 + - - +
63B LEU 3.3 1.9 + - - +
65B PHE* 1.3 86.6 - - + +
67B GLY* 1.3 62.2 + - - +
68B ALA 3.1 1.2 + - - -
69B PHE* 3.2 8.7 + - - +
70B ILE* 3.2 23.2 + - - +
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Residues in contact with GLY 67 (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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63B LEU* 2.6 28.0 + - - +
66B ALA* 1.3 70.9 - - - +
68B ALA* 1.3 60.3 + - - +
70B ILE* 3.7 4.3 - - - -
71B ILE* 3.0 32.6 + - - +
100B TRP* 3.3 16.2 - - - -
103B ILE* 3.8 15.0 - - - -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS 4.2 5.3 + - - +
65B PHE 3.1 7.6 + - - +
66B ALA 3.1 0.8 - - - -
67B GLY* 1.3 74.4 - - - +
69B PHE* 1.3 66.9 + - - +
71B ILE 3.4 0.9 + - - -
72B ASN* 3.0 29.2 + - - +
100B TRP* 3.8 8.8 - - + -
412B LEU* 3.8 5.9 - - + +
560B GLN* 4.0 17.3 - - - +
564B GLY* 4.4 2.2 - - - -
565B VAL* 3.2 38.4 - - + +
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 4.3 6.7 - + + -
15B THR* 3.3 35.2 - - + -
22B CYS* 3.6 18.2 - - - -
23B ARG* 4.1 9.6 - - - -
24B VAL* 3.5 29.8 - - + -
44B LEU* 4.1 13.6 - - + +
65B PHE* 3.5 29.8 - + - -
66B ALA* 3.2 8.9 + - - +
68B ALA* 1.3 77.5 - - - +
70B ILE* 1.3 61.5 + - - +
72B ASN* 3.5 2.8 + - - +
73B TRP* 3.3 21.1 + - - +
563B GLY 3.9 17.6 - - - +
564B GLY* 4.2 1.6 - - - -
565B VAL* 3.2 39.7 - - - -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.8 15.5 - - + -
44B LEU* 5.7 0.7 - - - -
47B PHE* 4.8 3.8 - - + -
48B MET* 4.1 21.0 - - + +
60B PHE* 3.8 26.7 - - + -
63B LEU* 5.1 0.2 - - + -
66B ALA 3.2 13.2 + - - +
67B GLY* 3.7 15.3 - - - +
68B ALA 3.1 0.4 - - - -
69B PHE* 1.3 76.0 - - - +
71B ILE* 1.3 65.0 + - - +
73B TRP* 3.1 7.3 + - - +
74B LEU* 3.0 37.2 + - + +
103B ILE* 4.1 8.5 - - + -
105B ILE* 4.8 0.4 - - + -
119B ILE* 3.3 37.5 - - + -
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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
----------------------------------------------------------
67B GLY 3.0 19.3 + - - +
70B ILE* 1.3 72.1 - - + +
72B ASN* 1.3 65.3 + - - +
74B LEU* 3.7 6.9 - - + +
75B GLU* 3.0 26.1 + - + +
90B TYR* 3.0 48.7 - - + +
92B THR* 3.9 15.3 - - + -
94B ILE* 5.4 0.2 - - + -
100B TRP* 4.0 17.5 - - + -
103B ILE* 4.2 12.6 - - + -
404B PRO* 4.1 12.1 - - + -
412B LEU* 3.9 26.9 - - + -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 3.0 18.9 + - - +
69B PHE 3.6 3.6 - - - +
70B ILE 3.2 0.2 - - - -
71B ILE* 1.3 77.8 - - - +
73B TRP* 1.3 60.0 + - - +
75B GLU* 3.8 3.0 + - - +
76B ARG* 3.1 40.2 + - - +
406B LEU* 4.5 2.7 - - - +
410B GLY 3.0 16.3 + - - -
411B ALA* 4.4 1.0 - - - +
412B LEU* 2.8 38.8 + - - +
560B GLN* 4.7 0.3 - - - +
561B VAL 4.2 1.6 + - - -
562B PRO 2.4 32.3 + - - -
563B GLY 3.3 17.7 + - - +
564B GLY* 4.1 3.9 - - - +
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Residues in contact with TRP 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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44B LEU* 4.1 18.8 - - + -
45B ASP* 3.9 33.4 + - - +
48B MET* 3.5 50.7 - - + -
49B ALA* 5.1 1.8 - - - -
52B LEU* 3.8 29.8 - - + -
69B PHE 3.3 10.4 + - - +
70B ILE* 3.1 8.8 + - - +
72B ASN* 1.3 78.0 - - - +
74B LEU* 1.3 81.9 + - + +
76B ARG* 3.3 5.4 + - - +
77B ASN* 2.6 67.3 + - + +
79B PHE* 5.0 2.5 - + - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B MET* 4.3 3.4 - - + -
52B LEU* 4.6 2.2 - - + -
70B ILE* 3.0 28.0 + - + +
71B ILE* 3.7 12.1 - - + +
73B TRP* 1.3 96.0 - - + +
75B GLU* 1.3 57.5 + - - +
77B ASN 3.0 17.3 + - - -
79B PHE* 3.1 51.8 + - + +
90B TYR* 3.8 29.8 - - + -
103B ILE* 4.4 6.1 - - + -
105B ILE* 3.9 36.1 - - + -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.0 23.5 + - + +
72B ASN* 4.0 2.9 - - - +
74B LEU* 1.3 76.3 - - - +
76B ARG* 1.3 59.7 + - - +
77B ASN 3.7 0.2 + - - -
78B GLY 4.5 2.9 + - - -
79B PHE 3.3 15.9 + - - +
80B LYS* 3.8 4.3 - - - +
81B TRP* 3.7 11.6 + - - +
90B TYR* 3.1 31.9 + - + +
404B PRO 4.7 0.5 - - - +
405B TYR* 4.4 6.0 - - - -
406B LEU* 3.7 49.6 + - + +
412B LEU* 4.7 1.6 - - + -
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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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72B ASN* 3.1 25.9 + - - +
73B TRP* 3.3 7.5 + - - +
74B LEU 3.2 0.8 - - - -
75B GLU* 1.3 77.0 - - - +
77B ASN* 1.3 69.8 + - - +
78B GLY 3.7 2.0 + - - -
406B LEU* 3.9 17.4 - - + +
410B GLY* 3.1 35.3 + - - -
562B PRO* 3.4 19.8 + - - +
563B GLY* 4.6 3.1 - - - +
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 2.6 74.4 + - + +
74B LEU 3.0 4.5 + - - +
76B ARG* 1.3 90.5 - - - +
78B GLY* 1.3 60.3 + - - +
79B PHE* 3.3 16.5 - - - -
88B ASN* 5.6 0.5 + - - -
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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