Contacts of the helix formed by residues 62 - 77 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PHE* 4.6 0.7 - - - -
61A HIS* 1.3 80.0 - - - +
63A LEU* 1.3 62.6 + - - +
64A LYS* 3.1 14.7 - - - +
65A PHE* 3.1 33.2 + - - +
66A ALA* 3.8 4.0 + - - +
121A ASP* 2.6 19.8 + - - +
123A LEU* 3.6 22.9 - - + +
3C T 2.6 34.7 + - - +
4C T 3.6 23.6 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 4.0 14.5 + - + -
61A HIS 3.8 0.2 - - - -
62A ASN* 1.3 66.6 - - - +
64A LYS* 1.3 57.0 + - - +
65A PHE 2.9 5.6 - - - -
66A ALA* 4.5 1.6 - - + +
67A GLY* 2.6 53.4 + - - +
70A ILE* 5.1 0.7 - - + -
100A TRP* 3.9 15.4 - - + -
101A TYR 4.1 2.7 - - - -
102A MET* 4.0 19.3 - - - +
103A ILE* 3.8 16.6 - - + -
119A ILE* 4.0 26.9 - - + +
120A TYR 3.8 23.1 - - - +
121A ASP* 2.9 27.8 + - + +
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Residues in contact with LYS 64 (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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62A ASN* 3.1 16.1 - - - +
63A LEU* 1.3 78.3 - - - +
65A PHE* 1.3 59.7 + - - +
68A ALA* 4.2 6.2 + - - +
97A MET 4.9 2.0 + - - -
98A GLY* 3.0 32.7 + - - +
99A GLN* 5.4 0.9 - - - -
100A TRP* 3.4 49.4 - - + +
121A ASP* 4.9 1.7 + - - +
402A LYS* 5.7 1.2 - - - +
558A PRO* 5.2 17.0 - - - -
560A GLN* 5.2 0.9 + - - -
565A VAL* 4.6 4.9 - - - +
3C T 5.8 7.0 - - - +
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Residues in contact with PHE 65 (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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13A PHE* 5.6 5.2 - - + -
15A THR* 3.5 30.7 - - + -
62A ASN* 3.1 24.0 + - - +
63A LEU 2.9 1.8 + - - -
64A LYS* 1.3 77.9 - - - +
66A ALA* 1.3 71.8 + - + +
67A GLY 3.2 1.1 - - - -
68A ALA* 3.1 19.8 + - - +
69A PHE* 3.5 22.3 - + - -
558A PRO* 5.9 1.1 - - + -
565A VAL* 3.9 38.1 - - + +
566A VAL* 5.1 0.9 - - - -
567A LEU* 4.5 12.6 - - + -
4C T 2.9 25.4 - + - +
5C T 3.8 31.9 - - - -
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Residues in contact with ALA 66 (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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13A PHE* 3.9 16.1 - - + +
60A PHE* 3.2 50.0 - - + -
61A HIS 6.2 0.2 - - - +
62A ASN 3.8 3.9 + - - +
63A LEU* 3.3 2.6 + - - +
65A PHE* 1.3 86.3 - - + +
67A GLY* 1.3 62.9 + - - +
68A ALA 3.1 1.0 + - - -
69A PHE* 3.1 15.6 + - - +
70A ILE* 3.2 16.3 + - - +
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Residues in contact with GLY 67 (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 LEU* 2.6 40.3 + - - +
66A ALA* 1.3 73.9 - - - +
68A ALA* 1.3 56.2 + - - +
69A PHE 3.3 0.2 - - - -
70A ILE* 3.7 3.5 - - - +
71A ILE* 2.9 35.5 + - - +
100A TRP* 3.5 13.7 - - - -
103A ILE* 3.8 7.2 - - - -
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Residues in contact with ALA 68 (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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64A LYS 4.2 4.7 + - - +
65A PHE 3.1 8.6 + - - +
67A GLY* 1.3 77.2 - - - +
69A PHE* 1.3 64.0 + - - +
72A ASN* 2.7 31.5 + - - -
100A TRP* 3.8 7.0 - - + -
412A LEU* 3.6 10.1 - - - +
560A GLN* 3.9 16.2 - - - +
564A GLY* 4.4 0.7 - - - -
565A VAL* 3.2 40.2 - - + +
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Residues in contact with PHE 69 (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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13A PHE* 4.3 7.4 - + + -
15A THR* 3.3 35.4 - - + -
22A CYS* 3.5 22.4 - - - -
23A ARG* 4.0 9.9 - - - -
24A VAL* 3.5 27.6 - - + -
44A LEU* 4.2 11.8 - - + +
65A PHE* 3.5 29.6 - + - -
66A ALA* 3.1 9.6 + - - +
68A ALA* 1.3 76.9 - - - +
70A ILE* 1.3 62.0 + - - +
72A ASN* 3.5 2.9 - - - +
73A TRP* 3.2 21.5 + - - +
563A GLY 3.6 19.6 - - - +
564A GLY* 4.2 0.2 - - - -
565A VAL* 3.3 35.7 - - - -
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Residues in contact with ILE 70 (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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13A PHE* 3.8 8.5 - - + -
47A PHE* 4.7 1.8 - - + -
48A MET* 3.3 32.0 - - + +
60A PHE* 3.8 28.7 - - + -
63A LEU* 5.1 0.2 - - + -
66A ALA 3.2 16.1 + - - +
67A GLY* 3.7 11.0 - - - +
68A ALA 3.2 0.2 - - - -
69A PHE* 1.3 75.5 - - - +
71A ILE* 1.3 65.7 + - - +
73A TRP* 3.1 5.2 + - - +
74A LEU* 3.0 39.0 + - + +
103A ILE* 4.2 7.2 - - + -
105A ILE* 4.8 2.2 - - + -
119A ILE* 3.5 35.4 - - + -
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Residues in contact with ILE 71 (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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67A GLY 2.9 22.0 + - - +
70A ILE* 1.3 72.4 - - - +
72A ASN* 1.3 65.8 + - - +
74A LEU* 3.7 6.7 - - + +
75A GLU* 2.9 28.0 + - + +
90A TYR* 3.0 50.7 - - + +
92A THR* 4.5 3.6 - - + -
94A ILE* 6.0 0.2 - - + -
100A TRP* 4.0 15.9 - - + -
103A ILE* 3.8 32.1 - - + -
404A PRO* 4.3 10.5 - - + -
412A LEU* 3.6 27.8 - - + -
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Residues in contact with ASN 72 (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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68A ALA 2.7 27.7 + - - +
69A PHE 3.5 4.0 - - - +
70A ILE 3.2 0.2 - - - -
71A ILE* 1.3 75.9 - - - +
73A TRP* 1.3 57.8 + - - +
75A GLU* 3.9 3.3 + - - +
76A ARG* 3.2 38.4 + - - +
406A LEU* 4.1 5.1 - - - +
410A GLY 3.0 26.2 - - - +
411A ALA* 4.4 1.2 - - - -
412A LEU* 3.5 25.5 - - - +
560A GLN* 4.6 1.0 + - - -
561A VAL 4.7 1.4 + - - -
563A GLY* 3.3 33.5 + - - +
564A GLY* 3.4 13.5 - - - +
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Residues in contact with TRP 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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44A LEU* 4.0 18.4 - - + -
45A ASP* 3.9 32.1 + - + +
48A MET* 3.3 47.4 - - + +
49A ALA* 5.0 1.8 - - - -
52A LEU* 3.9 28.9 - - + -
69A PHE 3.2 8.9 + - - +
70A ILE* 3.1 9.3 + - - +
71A ILE 3.1 0.4 - - - -
72A ASN* 1.3 78.6 - - - +
74A LEU* 1.3 88.1 + - + +
76A ARG* 3.1 10.0 + - - +
77A ASN* 2.8 61.4 + - + +
79A PHE* 4.9 2.7 - + - -
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Residues in contact with LEU 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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48A MET* 5.5 2.0 - - - -
52A LEU* 4.5 3.6 - - + -
70A ILE* 3.0 28.8 + - + +
71A ILE* 3.7 16.4 - - + +
73A TRP* 1.3 97.3 - - + +
75A GLU* 1.3 61.5 + - - +
77A ASN 3.0 13.2 + - - -
79A PHE* 3.1 51.6 + - + +
90A TYR* 3.8 31.0 - - + -
103A ILE* 4.5 0.9 - - + -
105A ILE* 3.9 34.5 - - + -
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Residues in contact with GLU 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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71A ILE* 2.9 24.2 + - + +
72A ASN* 4.2 2.7 - - - +
74A LEU* 1.3 76.8 - - - +
76A ARG* 1.3 59.9 + - - +
78A GLY 4.3 3.5 + - - -
79A PHE 3.4 15.5 + - - +
80A LYS* 3.9 3.3 - - - +
81A TRP* 3.8 10.6 + - - +
90A TYR* 3.1 32.8 + - + +
404A PRO 4.7 0.7 - - - +
405A TYR* 4.4 6.0 - - - +
406A LEU* 3.7 49.5 + - + +
412A LEU* 4.7 1.1 - - + -
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Residues in contact with ARG 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 ASN* 3.2 24.0 + - - +
73A TRP* 3.1 10.1 + - - +
75A GLU* 1.3 77.6 - - - +
77A ASN* 1.3 67.7 + - - +
78A GLY 3.6 2.2 + - - -
406A LEU* 3.9 19.1 - - + +
410A GLY* 3.0 35.6 + - - -
562A PRO* 4.3 3.2 - - - +
563A GLY* 3.6 21.8 - - - +
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Residues in contact with ASN 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 TRP* 2.8 73.6 + - + +
74A LEU 3.0 4.5 + - - +
76A ARG* 1.3 89.1 - - - +
78A GLY* 1.3 60.6 + - - +
79A PHE* 3.3 16.6 - - - -
88A ASN* 5.3 1.2 + - - -
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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