Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 1C7Y
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.8 6.5 - - - -
63A PHE* 3.3 4.5 - - - +
64A ASN* 1.3 92.2 - - - +
66A LYS* 1.3 67.4 + - - +
67A GLN* 3.9 13.2 - - - +
68A GLU* 2.6 42.8 + - + +
69A ARG* 3.0 18.7 + - - +
140A PHE* 3.7 26.8 - - + -
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Residues in contact with LYS 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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48A PHE* 3.7 33.5 - - + -
65A ASN* 1.3 74.5 - - - +
67A GLN* 1.3 74.4 + - - +
69A ARG* 3.0 31.1 + - - +
70A THR* 2.8 29.3 + - - +
145A ASP* 4.0 24.2 + - - +
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Residues in contact with GLN 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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65A ASN* 3.9 4.6 - - - +
66A LYS* 1.3 90.6 - - - +
68A GLU* 1.3 63.7 + - - +
70A THR* 2.9 10.3 + - - -
71A LEU* 2.9 25.5 + - - +
139A LEU* 3.7 26.4 - - + +
140A PHE* 2.8 38.7 - - + +
144A ALA* 3.5 29.8 - - + +
145A ASP* 4.0 10.5 + - - +
148A LEU* 4.2 5.2 - - + +
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Residues in contact with GLU 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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33A THR* 5.9 0.2 - - - -
34A CYS* 2.7 34.3 - - - +
37A GLU* 6.1 0.3 - - - +
63A PHE* 3.7 12.0 - - + -
64A ASN* 3.2 15.8 + - - +
65A ASN* 2.6 47.8 + - + +
67A GLN* 1.3 77.0 - - - +
69A ARG* 1.3 61.5 + - - +
71A LEU* 3.7 6.9 + - - +
72A PHE* 3.2 22.0 + - - +
90A LEU* 4.5 5.4 - - + +
95A ALA* 4.8 19.1 - - + -
139A LEU* 5.2 0.6 - - + +
140A PHE* 4.8 6.2 - - + -
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Residues in contact with ARG 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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3A GLY* 2.9 22.6 + - - -
48A PHE* 3.6 27.8 - - + +
49A THR 2.6 42.9 + - - +
50A HIS* 4.6 1.8 - - + -
63A PHE* 3.4 33.2 - - + +
65A ASN 3.0 10.0 + - - +
66A LYS* 3.0 26.9 + - - +
68A GLU* 1.3 76.6 - - - +
70A THR* 1.3 53.9 + - - +
72A PHE* 3.2 6.2 + - - +
73A LYS* 2.8 70.8 + - - +
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Residues in contact with THR 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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66A LYS* 2.8 17.0 + - - +
67A GLN 2.9 7.6 + - - -
69A ARG* 1.3 76.2 + - - +
71A LEU* 1.3 65.5 + - - +
73A LYS* 3.1 10.1 + - + +
74A GLU* 2.9 31.5 + - - +
145A ASP* 3.0 28.8 - - + +
148A LEU* 3.4 30.7 - - + -
149A THR* 4.1 16.6 - - - +
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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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67A GLN 2.9 17.5 + - - +
68A GLU* 3.9 4.0 - - - +
70A THR* 1.3 72.9 - - - +
72A PHE* 1.3 58.8 + - - +
74A GLU* 3.1 9.4 + - - +
75A LEU* 2.8 39.5 + - + +
90A LEU* 3.8 21.3 - - + -
95A ALA* 3.6 39.5 - - + +
98A PHE* 3.8 17.0 - - + -
99A VAL* 5.0 3.4 - - + -
128A MET* 5.1 2.7 - - - -
132A PHE* 3.3 38.4 - - + -
139A LEU* 5.5 4.3 - - + -
148A LEU* 4.2 9.3 - - + +
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Residues in contact with PHE 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 PRO* 5.5 0.2 - - + -
50A HIS* 3.7 30.5 - + - -
61A TYR* 3.8 24.5 - + + -
63A PHE* 3.1 37.0 - + + -
68A GLU 3.2 11.9 + - - +
69A ARG 3.2 8.8 + - - +
71A LEU* 1.3 80.9 - - - +
73A LYS* 1.3 60.3 + - - +
75A LEU* 3.1 10.5 + - - +
76A ILE* 2.9 43.9 + - + +
83A PRO* 3.6 27.6 - - + -
86A ALA* 3.5 31.4 - - + -
87A LEU* 4.1 8.1 - - + -
90A LEU* 4.2 7.0 - - + -
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Residues in contact with LYS 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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49A THR 5.2 1.0 + - - -
50A HIS* 2.9 44.6 - - + +
69A ARG* 2.8 48.1 + - - +
70A THR* 3.1 11.4 + - - +
72A PHE* 1.3 70.2 - - + +
74A GLU* 1.3 70.4 + - - +
76A ILE* 2.9 27.7 - - + +
77A LYS* 3.4 17.4 + - - +
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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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70A THR* 2.9 28.7 + - + +
71A LEU* 3.5 8.1 - - + +
73A LYS* 1.3 76.6 - - - +
75A LEU* 1.3 68.2 + - - +
77A LYS* 3.0 47.5 + - - +
78A THR 3.3 2.9 + - - -
128A MET* 3.2 28.6 - - + +
131A ARG* 3.2 32.2 + - + +
132A PHE* 6.3 0.2 - - + -
148A LEU* 4.6 13.9 - - + +
149A THR* 3.7 25.9 + - - -
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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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71A LEU* 2.8 28.6 + - + +
72A PHE* 3.1 16.4 + - - +
74A GLU* 1.3 75.9 - - - +
76A ILE* 1.3 63.7 + - - +
78A THR* 3.1 15.9 + - - -
81A VAL* 3.0 20.8 - - + +
86A ALA* 4.0 21.3 - - + -
89A ILE* 4.6 10.8 - - + -
90A LEU* 3.9 25.4 - - + -
98A PHE* 3.5 37.7 - - + -
124A LEU* 3.5 15.7 - - + -
128A MET* 3.6 10.3 - - + -
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Residues in contact with ILE 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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50A HIS* 3.4 36.1 - - + +
72A PHE* 2.9 38.9 + - + +
73A LYS* 2.9 34.5 - - + +
75A LEU* 1.3 73.2 - - - +
77A LYS* 1.3 69.1 + - + +
81A VAL* 2.9 23.9 - - - +
82A GLY* 4.0 22.6 - - - +
83A PRO* 4.0 7.0 - - + -
86A ALA* 4.2 3.1 - - + -
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Residues in contact with LYS 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 LYS* 3.5 18.7 - - - +
74A GLU* 3.0 42.9 + - - +
76A ILE* 1.3 84.5 - - + +
78A THR* 1.3 65.3 + - - +
79A ASN* 3.3 3.6 + - - -
131A ARG* 4.7 11.0 - - - +
149A THR* 5.2 4.9 + - - -
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Residues in contact with THR 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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74A GLU 3.3 1.0 + - - -
75A LEU* 3.1 15.3 + - - -
77A LYS* 1.3 80.1 - - - +
79A ASN* 1.3 75.4 + - + +
80A GLY 3.5 0.2 + - - -
81A VAL* 3.1 26.8 + - + +
123A ARG* 4.5 15.5 - - + +
124A LEU* 4.2 30.1 - - + +
127A GLU* 4.7 18.5 - - + +
128A MET* 3.3 25.1 - - - +
131A ARG* 5.4 0.7 + - - +
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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