Contacts of the helix formed by residues 65 - 77 (chain A) in PDB entry 4CGS
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 PRO 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP 4.7 1.1 - - - +
64A THR* 1.3 90.5 + - - +
66A PRO* 1.4 73.0 - - + +
67A GLU* 3.7 13.5 - - - +
68A VAL* 3.0 27.6 + - + +
69A ALA* 3.1 9.7 + - - +
82B ARG* 6.0 1.6 - - - +
111B TYR* 3.7 24.5 - - + -
112B GLN* 3.4 38.1 - - + +
121B ARG* 5.7 0.2 - - - +
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Residues in contact with PRO 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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64A THR 3.5 4.7 - - - +
65A PRO* 1.4 82.3 - - + +
67A GLU* 1.3 68.2 + - - +
69A ALA* 3.3 8.8 + - + +
70A ASP* 2.8 29.4 + - - +
85A VAL* 4.6 19.4 - - + +
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Residues in contact with GLU 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 PRO* 3.7 9.4 - - - +
66A PRO* 1.3 91.0 - - + +
68A VAL* 1.3 57.8 + - - +
70A ASP* 3.5 8.1 + - - +
71A GLN* 3.0 31.4 + - - +
111B TYR* 3.3 48.0 - - + +
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Residues in contact with VAL 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 THR* 4.6 13.0 - - + +
65A PRO* 3.0 29.4 + - + +
67A GLU* 1.3 74.5 - - - +
69A ALA* 1.3 65.0 + - - +
71A GLN* 3.0 28.7 + - - +
72A GLU* 3.0 26.6 + - + +
100B LYS* 5.7 8.3 - - - -
111B TYR* 4.0 16.2 - - + -
119B PHE* 6.5 0.7 - - + -
121B ARG* 3.6 27.6 - - - +
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Residues in contact with ALA 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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61A ASN* 3.6 36.3 - - + +
64A THR* 4.2 4.6 + - - +
65A PRO 3.1 11.1 + - - +
66A PRO* 3.6 8.5 - - + +
68A VAL* 1.3 77.8 - - - +
70A ASP* 1.3 58.1 + - - +
72A GLU* 3.2 4.3 + - - +
73A MET* 2.8 38.5 + - + +
85A VAL* 3.9 20.6 - - + -
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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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66A PRO 2.8 18.3 + - - +
67A GLU* 3.6 9.4 - - - +
68A VAL 3.2 0.2 - - - -
69A ALA* 1.3 76.2 - - - +
71A GLN* 1.3 62.4 + - - +
73A MET* 3.3 19.9 + - + +
74A LYS* 2.9 51.6 + - - +
79A ILE* 6.0 1.0 - - - +
85A VAL* 6.0 0.2 - - + -
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Residues in contact with GLN 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 GLU* 3.0 17.9 + - - +
68A VAL* 3.0 24.3 + - - +
70A ASP* 1.3 73.6 - - - +
72A GLU* 1.3 58.3 + - + +
74A LYS* 3.5 6.7 + - - +
75A ARG* 2.9 32.5 + - - +
100B LYS* 5.7 2.6 - - - +
102B TYR* 4.1 31.8 + - - -
111B TYR* 3.8 28.1 + - - -
121B ARG* 5.2 0.5 + - - -
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Residues in contact with GLU 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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59A ILE* 3.7 33.8 - - + +
61A ASN* 4.3 9.2 - - - +
68A VAL* 3.0 29.9 + - + +
69A ALA* 3.4 11.2 - - - +
71A GLN* 1.3 76.4 - - + +
73A MET* 1.3 58.1 + - - +
75A ARG* 3.3 12.5 + - - +
76A GLN* 3.0 36.4 + - - +
89A LEU* 4.2 10.5 - - + -
100B LYS* 5.9 3.1 - - - -
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Residues in contact with MET 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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61A ASN* 4.8 2.7 - - - +
69A ALA* 2.8 30.7 + - + +
70A ASP* 3.7 20.6 - - + +
72A GLU* 1.3 72.7 - - - +
74A LYS* 1.3 57.7 + - - +
76A GLN* 3.3 1.1 + - - -
77A ASN* 2.9 24.1 + - - -
78A LEU 3.0 26.8 + - - +
79A ILE* 3.5 7.0 - - + +
80A PHE* 3.7 28.9 - - - -
85A VAL* 3.6 31.0 - - + -
86A PRO* 3.8 14.6 - - - -
89A LEU* 3.9 22.7 - - + -
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Residues in contact with LYS 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 ASP* 2.9 47.5 + - - +
71A GLN* 3.8 6.5 - - - +
73A MET* 1.3 75.4 - - - +
75A ARG* 1.3 63.9 + - - +
77A ASN* 3.2 12.6 + - - +
79A ILE* 4.0 15.4 - - + +
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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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71A GLN 2.9 19.8 + - - +
72A GLU* 3.3 12.8 + - - +
74A LYS* 1.3 77.6 - - - +
76A GLN* 1.3 68.7 + - + +
77A ASN* 3.6 1.0 + - - +
26B ASN* 3.4 27.4 - - - +
32B ALA* 5.5 1.6 - - - +
167B LEU* 3.2 46.7 + - - +
168B TYR* 4.0 22.7 - - - +
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Residues in contact with GLN 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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59A ILE* 3.9 15.9 - - + +
72A GLU* 3.0 21.9 + - - +
73A MET 4.1 1.8 - - - +
75A ARG* 1.3 87.3 + - + +
77A ASN* 1.3 61.8 + - - +
78A LEU* 3.9 18.8 - - + -
89A LEU* 4.6 2.2 - - + -
91A LEU* 3.7 37.5 - - + +
94A ARG* 2.8 36.2 + - - -
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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 MET 2.9 7.1 + - - -
74A LYS 3.2 12.3 + - - +
75A ARG 3.3 1.3 - - - +
76A GLN* 1.3 79.3 - - - +
78A LEU* 1.3 58.0 - - - +
79A ILE* 3.9 17.8 + - - +
94A ARG* 2.9 18.0 + - - +
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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