Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 1CP3
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASN* 2.5 37.5 + - - +
53A LYS* 3.7 32.1 - - + -
64A ARG* 2.8 47.5 + - - +
65A SER 3.3 1.2 + - - -
66A GLY* 1.3 77.7 - - - +
68A ASP* 1.3 58.5 + - - +
69A VAL 3.3 0.2 - - - -
70A ASP* 3.3 12.2 + - - +
71A ALA 2.9 23.6 + - - -
119A LEU* 3.9 5.9 - - - +
207A ARG* 4.2 3.7 - - - +
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Residues in contact with ASP 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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51A ASN* 3.6 15.4 - - - +
53A LYS* 2.9 37.4 + - - +
66A GLY* 3.0 3.6 + - - +
67A THR* 1.3 78.3 - - - +
69A VAL* 1.3 66.2 + - + +
71A ALA* 3.6 6.5 + - - +
72A ALA* 3.1 23.9 + - - +
89A ASN* 5.2 1.4 + - - -
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Residues in contact with VAL 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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66A GLY* 3.1 16.3 + - - +
68A ASP* 1.3 78.0 - - + +
70A ASP* 1.3 57.4 + - - +
72A ALA* 3.3 5.4 + - - +
73A ASN* 2.9 36.8 + - + +
210A LYS 3.6 21.1 - - - +
211A ASP* 3.5 23.3 - - - +
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Residues in contact with ASP 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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64A ARG* 5.3 1.0 + - - -
66A GLY 3.5 2.9 + - - -
67A THR* 3.3 15.1 + - - +
68A ASP 3.2 0.2 - - - -
69A VAL* 1.3 74.8 - - - +
71A ALA* 1.3 66.1 + - - +
72A ALA 3.0 0.5 + - - -
73A ASN* 3.7 3.0 - - - +
74A LEU* 3.0 29.7 + - - +
119A LEU* 4.0 14.9 - - + +
161A GLN* 4.7 0.9 - - - +
207A ARG* 5.1 1.6 - - - -
211A ASP 4.3 1.9 - - - +
212A GLY* 3.4 9.4 - - - -
213A SER* 2.5 48.7 + - - +
216A ILE* 3.6 24.5 - - + +
217A GLN* 4.6 3.3 + - - +
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Residues in contact with ALA 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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49A ILE* 4.1 6.4 - - + +
51A ASN* 3.7 32.5 - - + +
67A THR 2.9 11.6 + - - +
68A ASP* 3.9 6.7 - - - +
69A VAL 3.5 0.2 - - - -
70A ASP* 1.3 76.0 - - - +
72A ALA* 1.3 60.2 + - - +
74A LEU* 3.8 2.7 - - - +
75A ARG* 3.3 21.8 + - - +
87A ASN* 3.6 20.9 + - - +
89A ASN* 5.0 1.6 - - - +
119A LEU* 3.8 8.4 - - - +
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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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68A ASP 3.1 18.9 + - - +
69A VAL* 3.6 5.6 - - - +
70A ASP 3.1 0.2 - - - -
71A ALA* 1.3 75.3 - - - +
73A ASN* 1.3 66.3 + - - +
75A ARG* 3.4 7.8 + - - +
76A GLU* 3.2 24.1 + - - +
87A ASN* 5.4 0.4 - - - +
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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 VAL* 2.9 21.7 + - + +
70A ASP* 3.7 5.2 - - - +
72A ALA* 1.3 74.8 - - - +
74A LEU* 1.3 60.7 + - - +
76A GLU* 3.4 6.0 + - - +
77A THR* 2.7 34.2 + - - -
216A ILE* 4.5 4.0 - - + +
217A GLN* 4.5 9.9 - - - +
220A CYS* 3.5 21.1 - - - +
224A LYS* 3.5 33.0 + - - +
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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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49A ILE* 3.7 18.4 - - + -
70A ASP 3.0 19.8 + - - +
71A ALA 3.8 0.7 - - - +
73A ASN* 1.3 76.9 - - - +
75A ARG* 1.3 57.4 + - - +
77A THR* 4.3 0.7 - - - -
78A PHE* 3.0 60.2 + - + +
117A VAL* 3.5 34.8 - - + -
119A LEU* 4.0 17.9 - - + -
216A ILE* 3.6 22.2 - - + -
219A LEU* 4.4 13.2 - - + -
220A CYS* 3.7 16.8 - - - -
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Residues in contact with ARG 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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49A ILE* 3.8 7.6 - - + +
71A ALA 3.3 15.8 + - - +
72A ALA* 3.7 8.1 - - - +
73A ASN 3.3 0.4 - - - -
74A LEU* 1.3 79.4 - - - +
76A GLU* 1.3 57.7 + - - +
79A ARG* 3.1 30.5 + - + +
85A VAL* 3.9 35.9 + - + +
86A ARG* 4.5 0.4 - - - +
87A ASN* 3.1 43.1 + - - +
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Residues in contact with GLU 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 ALA 3.2 14.6 + - - +
73A ASN* 3.9 5.6 - - - +
75A ARG* 1.3 77.5 - - - +
77A THR* 1.3 61.9 + - - +
79A ARG* 2.7 42.6 + - - +
80A ASN* 2.7 52.9 + - - +
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Residues in contact with THR 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* 2.7 27.0 + - - -
74A LEU* 3.7 4.3 - - - -
76A GLU* 1.3 78.9 - - - +
78A PHE* 1.3 64.6 + - + +
80A ASN* 3.3 10.3 + - - +
81A LEU* 3.3 23.6 + - + +
220A CYS* 3.5 30.2 - - - +
223A LEU* 3.8 39.7 - - + -
224A LYS* 3.9 14.2 - - + +
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Residues in contact with PHE 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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47A CYS* 3.9 27.6 - - - -
74A LEU* 3.0 55.2 + - + +
77A THR* 1.3 77.5 - - + +
79A ARG* 1.3 62.4 + - - +
81A LEU* 3.5 13.8 + - + -
82A LYS 3.3 2.9 + - - -
83A TYR* 2.8 53.9 + + + +
85A VAL* 4.1 8.1 - - + -
115A VAL* 4.0 20.9 - - + -
117A VAL* 4.9 1.6 - - + -
157A LEU* 5.9 1.6 - - + -
159A ILE* 3.8 24.7 - - + -
219A LEU* 4.7 0.7 - - + -
223A LEU* 3.9 26.2 - - + -
232A PHE* 6.2 1.6 - + - -
275A PHE* 5.2 7.9 - + - -
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Residues in contact with ARG 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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75A ARG* 3.1 23.6 + - + +
76A GLU* 2.7 41.4 + - - +
77A THR 3.2 0.4 - - - -
78A PHE* 1.3 75.7 - - - +
80A ASN* 1.3 73.1 + - - +
82A LYS* 2.8 26.7 + - - +
83A TYR 4.2 10.7 - - - +
85A VAL* 4.5 4.3 - - + -
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Residues in contact with ASN 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 GLU* 2.7 46.9 + - - +
77A THR* 3.3 10.2 + - - +
79A ARG* 1.3 90.6 + - - +
81A LEU* 1.3 59.2 + - + +
82A LYS* 3.2 23.1 + - - +
224A LYS* 5.9 4.4 - - - +
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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