Contacts of the helix formed by residues 67 - 79 (chain A) in PDB entry 1X3B
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 ASP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 2.6 17.7 + - + +
64A LEU 3.0 16.9 - - - +
66A GLY* 1.3 70.0 - - - -
68A ALA* 1.3 63.5 + - - +
69A LYS* 4.0 19.2 - - - +
70A GLU* 4.1 30.7 - - + +
71A LEU 3.3 9.9 + - - -
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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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30A SER* 4.7 21.1 - - - +
31A ALA* 5.2 2.6 - - - +
66A GLY 3.3 4.8 + - - +
67A ASP* 1.3 73.7 - - - +
69A LYS* 1.3 61.1 + - - +
71A LEU* 2.6 29.8 + - + +
72A ALA* 2.7 18.9 + - - +
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Residues in contact with LYS 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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67A ASP* 4.0 13.4 + - - +
68A ALA* 1.3 80.5 - - - +
70A GLU* 1.3 63.6 - - + +
72A ALA* 3.6 4.3 + - - +
73A ASN* 3.0 22.0 + - - +
76A LYS* 5.4 8.5 - - - +
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Residues in contact with GLU 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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60A GLU* 5.3 2.4 - - - +
63A ARG* 4.4 29.0 + - - +
64A LEU* 4.4 11.2 - - + +
67A ASP* 4.0 31.5 + - + +
68A ALA 3.2 0.4 - - - -
69A LYS* 1.3 74.9 - - + +
71A LEU* 1.3 67.3 + - - +
73A ASN* 3.0 25.4 - - - +
74A ILE* 3.2 13.2 + - - +
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Residues in contact with LEU 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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27A ALA* 3.7 39.9 - - + +
30A SER* 4.3 13.5 - - - -
31A ALA* 4.8 1.8 - - + +
64A LEU* 3.0 44.4 - - + +
65A LEU* 4.6 7.6 - - + +
66A GLY 5.6 0.2 - - - +
67A ASP 3.3 12.9 + - - +
68A ALA* 2.6 20.4 + - + +
70A GLU* 1.3 69.5 - - - +
72A ALA* 1.3 57.3 + - - +
73A ASN 2.9 0.9 - - - -
74A ILE* 2.7 27.0 + - - +
75A LEU* 3.0 33.1 + - + -
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Residues in contact with ALA 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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31A ALA* 3.5 37.5 - - + +
33A LEU* 4.4 3.1 - - + -
68A ALA 2.7 16.8 + - - +
69A LYS* 4.1 4.3 - - - +
71A LEU* 1.3 73.0 - - - +
73A ASN* 1.3 51.3 + - - +
75A LEU* 3.0 3.9 + - - +
76A LYS* 2.5 59.4 + - - +
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Residues in contact with ASN 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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69A LYS 3.0 14.7 + - - +
70A GLU* 3.0 22.9 - - - +
71A LEU 2.8 1.0 + - - -
72A ALA* 1.3 76.7 - - - +
74A ILE* 1.3 64.6 + - + +
76A LYS* 3.2 6.9 + - - +
77A TYR 3.0 17.0 + - - -
99A GLN* 2.7 56.5 + - - +
140A PRO* 6.0 1.7 - - - +
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Residues in contact with ILE 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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60A GLU* 4.1 9.0 - - - +
64A LEU* 4.1 30.7 - - + -
70A GLU 3.6 10.8 - - - +
71A LEU 2.7 12.6 + - - +
73A ASN* 1.3 73.3 - - + +
75A LEU* 1.3 68.3 + - + +
77A TYR* 2.9 8.4 + - + +
78A HIS* 2.8 54.8 + - + +
99A GLN* 4.8 0.2 - - - +
137A VAL* 4.6 6.3 - - + -
138A LEU 4.5 6.7 - - - +
139A GLN* 4.8 2.2 - - + -
140A PRO* 3.2 39.5 - - + -
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Residues in contact with LEU 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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24A LEU* 4.4 14.4 - - + -
27A ALA* 3.2 36.6 - - + +
28A ILE* 3.3 25.4 - - + +
31A ALA* 3.4 11.7 - - + -
33A LEU* 3.4 17.7 - - + -
64A LEU* 6.2 0.2 - - + -
71A LEU* 3.0 25.5 + - + +
72A ALA* 3.4 3.1 - - - +
74A ILE* 1.3 83.9 - - + +
76A LYS* 1.3 52.5 + - - +
78A HIS* 2.7 29.2 + - + +
79A ILE* 2.7 29.6 + - + +
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Residues in contact with LYS 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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33A LEU* 4.6 17.0 - - + -
69A LYS* 5.4 8.7 - - - +
72A ALA* 2.5 42.1 + - - +
73A ASN* 3.3 11.9 - - - +
75A LEU* 1.3 73.3 - - - +
77A TYR* 1.3 54.2 + - - +
79A ILE* 2.7 35.5 + - - +
98A LEU* 3.8 12.8 + - + +
99A GLN* 3.4 35.4 + - + +
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Residues in contact with TYR 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 ASN 3.0 3.6 + - - -
74A ILE* 2.9 10.9 + - + +
76A LYS* 1.3 77.4 - - - +
78A HIS* 1.3 60.9 + + - +
79A ILE 3.3 0.2 - - - -
97A SER* 4.2 3.8 - - - -
99A GLN* 3.4 22.6 - - - +
101A ASP* 3.4 42.4 - - + -
102A LYS 4.8 5.1 + - - -
103A LEU* 2.7 49.3 - - + +
115A ASN* 3.1 39.3 + - - +
138A LEU* 4.1 6.9 - - + +
139A GLN 3.2 35.0 + - - -
140A PRO* 3.7 19.3 - - + +
141A SER 4.8 2.9 + - - -
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Residues in contact with HIS 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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24A LEU* 6.4 2.0 - - + -
44A THR 3.1 11.1 - - - +
45A VAL* 3.2 16.9 - - + -
46A PHE* 3.2 42.6 + - + +
48A PRO* 5.1 1.5 - - + +
74A ILE* 2.8 29.0 + - + +
75A LEU* 2.7 18.2 + - + +
77A TYR* 1.3 82.2 - + - +
79A ILE* 1.3 59.7 + - - +
103A LEU* 4.3 1.8 - - - -
134A ILE* 3.6 6.1 - - + +
137A VAL* 3.7 15.9 - - + +
138A LEU* 2.9 70.6 + - + +
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Residues in contact with ILE 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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28A ILE* 5.7 2.7 - - + -
33A LEU* 3.6 30.3 - - + -
37A LEU* 4.0 22.7 - - + -
43A TYR* 4.0 4.0 - - + -
44A THR 3.1 4.5 - - - -
45A VAL* 3.3 39.3 - - + -
75A LEU* 2.7 33.9 + - + +
76A LYS* 2.7 22.1 - - - +
78A HIS* 1.3 78.9 - - - +
80A GLY* 1.3 73.1 + - - +
97A SER* 3.5 14.9 - - - -
98A LEU* 3.7 18.9 + - + -
103A LEU* 3.6 3.2 - - - +
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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
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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