Contacts of the helix formed by residues 67 - 75 (chain A) in PDB entry 3C3P
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 GLY 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 3.0 25.3 + - - -
65A GLY 3.0 3.0 + - - -
66A LEU* 1.3 77.7 - - - +
68A CYS* 1.3 59.3 + - - +
70A SER* 3.4 4.0 + - - -
71A TRP* 2.9 30.3 + - - +
85A MSE 3.8 5.8 - - - +
96A ALA* 3.7 20.3 - - - +
99A MSE 3.8 4.3 - - - +
100A LEU* 6.2 0.2 - - - +
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Residues in contact with CYS 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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27A MSE 3.6 34.3 - - - -
38A ILE* 4.0 16.4 - - + -
39A VAL* 3.8 37.0 - - + +
64A ASP* 3.4 1.5 + - - +
65A GLY 3.0 15.8 + - - +
66A LEU 3.1 1.6 - - - -
67A GLY* 1.3 79.5 - - - +
69A ALA* 1.3 62.6 + - - +
71A TRP* 3.2 9.9 + - - +
72A TRP* 3.0 34.3 + - - -
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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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39A VAL* 4.9 4.2 - - + +
47A LEU* 4.5 6.3 - - + -
61A VAL* 4.0 7.6 - - + -
64A ASP* 2.9 19.4 + - - +
68A CYS* 1.3 77.2 - - - +
70A SER* 1.3 63.2 + - - +
72A TRP* 3.1 10.1 + - - +
73A PHE* 3.0 33.5 + - + -
130A PHE* 3.8 38.1 - - + -
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Residues in contact with SER 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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61A VAL* 3.8 9.2 - - - +
64A ASP* 2.7 23.3 + - - -
67A GLY* 3.7 6.3 - - - -
68A CYS 3.3 0.2 - - - -
69A ALA* 1.3 74.1 - - - +
71A TRP* 1.3 60.7 + - - +
73A PHE* 4.0 3.7 - - - +
74A ALA* 2.8 34.2 + - - +
83A VAL* 4.1 17.8 - - - +
85A MSE 3.1 29.9 - - - +
96A ALA* 5.7 0.2 - - - -
100A LEU* 5.3 7.0 - - - -
109A VAL* 5.0 7.6 - - - -
111A LEU* 5.4 0.7 - - - -
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Residues in contact with TRP 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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21A ASP* 3.5 17.3 - - - -
23A VAL* 3.6 20.9 - - + +
24A VAL* 3.1 33.9 - - + -
27A MSE 4.5 5.6 - - + -
67A GLY 2.9 17.8 + - - +
68A CYS* 3.4 7.6 - - - +
69A ALA 3.1 0.4 - - - -
70A SER* 1.3 80.1 - - - +
72A TRP* 1.3 90.3 + + - +
74A ALA* 3.9 4.6 - - - +
75A ARG* 3.0 66.7 + - - +
99A MSE 3.8 33.0 - - + +
100A LEU* 4.7 8.9 - - + +
103A ASN* 3.6 25.2 - - - +
219A PEG 3.7 9.4 - - - -
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Residues in contact with TRP 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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24A VAL* 4.4 16.1 - - + +
27A MSE 4.8 1.8 - - - +
39A VAL* 4.4 7.6 + - + +
41A ARG* 4.3 14.4 - - + -
44A GLY* 3.3 45.8 - - - +
45A ARG* 3.9 16.4 - - + -
47A LEU* 4.4 11.4 - - + -
48A TYR* 3.8 24.1 - + + +
68A CYS* 3.0 43.5 + - - -
69A ALA* 3.1 7.8 + - - +
71A TRP* 1.3 99.7 - + - +
73A PHE* 1.3 62.2 - - - +
75A ARG* 3.5 15.0 + - - +
76A ALA* 3.7 5.0 + - - +
210A CL 3.8 22.0 - - + -
219A PEG 3.5 31.0 - - - -
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Residues in contact with PHE 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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47A LEU* 4.0 38.6 - - + -
51A ALA* 4.0 15.9 - - + -
59A VAL* 3.9 20.2 - - + -
61A VAL* 4.1 6.1 - - + -
69A ALA* 3.0 30.3 + - + +
70A SER* 4.0 2.0 - - - +
72A TRP* 1.3 75.6 - - - +
74A ALA* 1.3 65.5 + - - +
76A ALA* 3.0 15.3 + - - +
77A ILE* 3.5 17.8 - - - +
83A VAL* 3.9 17.3 - - + -
128A ILE* 4.2 18.2 - - + -
130A PHE* 3.6 40.2 - + + -
156A ILE* 4.1 17.5 - - + -
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Residues in contact with ALA 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 SER 2.8 22.8 + - - +
71A TRP 3.9 2.7 - - - +
73A PHE* 1.3 73.8 - - - +
75A ARG* 1.3 62.0 + - - +
76A ALA 3.1 0.9 + - - -
77A ILE* 3.6 18.0 + - - +
83A VAL* 3.9 8.7 - - - +
100A LEU* 3.9 15.7 - - + -
105A LEU* 4.0 15.6 - - + +
108A ARG* 3.8 12.0 - - + -
109A VAL* 3.6 27.4 - - + -
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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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21A ASP* 3.2 25.1 + - - -
48A TYR* 3.6 18.0 + - + -
71A TRP* 3.0 57.5 - - + +
72A TRP* 3.6 9.0 - - - +
73A PHE 3.1 0.4 - - - -
74A ALA* 1.3 76.8 - - - +
76A ALA* 1.3 58.9 + - - +
77A ILE 3.5 0.7 - - - -
103A ASN* 5.5 1.3 - - - +
105A LEU* 3.9 21.4 - - + +
211A EDO 3.8 15.1 + - - -
219A PEG 3.1 37.0 + - - -
220A PEG 3.4 32.7 + - - -
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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