Contacts of the helix formed by residues 67 - 78 (chain A) in PDB entry 1V72
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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65A VAL* 3.5 10.1 - - - +
66A PRO* 1.3 92.3 - - + +
68A GLY* 1.3 60.3 + - - +
69A THR* 3.6 4.4 + - - -
70A ALA* 3.1 25.6 + - - +
71A ALA* 3.1 21.3 + - - +
219A GLU* 3.5 8.7 - - - -
241A HIS* 4.6 4.7 - - + -
513A PLP 3.7 18.4 - - - +
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Residues in contact with GLY 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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67A THR* 1.3 70.3 - - - +
69A THR* 1.3 64.0 + - - +
71A ALA* 3.6 6.3 - - - +
72A ASN* 3.0 32.3 + - - +
181A SER* 6.2 0.4 - - - -
207A SER* 5.8 1.6 - - - -
219A GLU* 3.5 19.7 - - - +
513A PLP 2.9 31.9 + - - -
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Residues in contact with THR 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 THR* 4.0 4.3 - - - -
68A GLY* 1.3 77.3 - - - +
70A ALA* 1.3 62.4 + - - +
72A ASN* 3.4 1.9 + - - +
73A ALA* 3.0 23.4 + - - +
93A HIS* 3.7 7.3 - - - -
97A ASP 4.4 2.3 + - - -
98A GLU* 3.5 36.5 - - + +
101A ALA* 3.4 27.8 - - + -
105A PHE* 5.9 0.9 - - + -
513A PLP 2.6 26.1 + - - -
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Residues in contact with ALA 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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65A VAL* 4.5 3.8 - - + -
67A THR* 3.1 20.2 + - - +
69A THR* 1.3 77.0 - - - +
71A ALA* 1.3 64.5 + - - +
73A ALA* 4.0 0.2 - - - +
74A LEU* 2.9 35.2 + - + +
105A PHE* 4.6 9.4 - - - -
241A HIS* 3.4 46.7 - - + +
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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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65A VAL* 3.9 13.4 - - + +
67A THR 3.1 14.1 + - - +
68A GLY* 3.6 11.2 - - - +
70A ALA* 1.3 76.5 - - - +
72A ASN* 1.3 60.5 + - - +
74A LEU* 3.9 1.2 - - - +
75A CYS* 3.1 30.0 + - - -
207A SER* 3.5 23.1 - - - +
219A GLU* 4.6 7.4 - - + -
220A ALA 5.2 1.1 - - - +
221A ILE* 3.9 18.3 - - + +
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Residues in contact with ASN 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 GLY 3.0 18.3 + - - +
69A THR 3.7 4.5 - - - +
71A ALA* 1.3 74.0 - - - +
73A ALA* 1.3 66.1 + - - +
75A CYS* 3.2 3.3 + - - +
76A LEU* 3.0 30.4 + - - +
94A ILE* 3.7 15.9 - - + +
98A GLU* 2.8 26.0 + - - +
177A HIS* 3.5 10.9 - - + -
179A ASP* 3.0 34.3 + - - +
207A SER* 2.7 33.0 + - - -
513A PLP 3.8 6.7 - - - -
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Residues in contact with ALA 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 THR 3.0 13.8 + - - +
70A ALA 4.0 0.9 - - - +
72A ASN* 1.3 79.1 - - - +
74A LEU* 1.3 58.6 + - - +
76A LEU* 3.8 2.8 - - - +
77A SER* 2.9 31.9 + - - -
98A GLU* 4.6 0.6 + - - -
101A ALA* 3.7 19.3 - - + +
102A PRO* 4.1 11.0 - - - +
105A PHE* 3.4 40.5 - - + +
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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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65A VAL* 3.9 18.2 - - + -
70A ALA* 2.9 25.1 + - + +
73A ALA* 1.3 75.8 - - - +
75A CYS* 1.3 63.8 + - - +
77A SER* 2.7 18.9 + - - +
78A ALA* 3.3 4.5 + - - +
105A PHE* 3.6 23.8 - - + -
221A ILE* 3.7 26.9 - - + -
232A MET* 3.5 15.5 - - - +
235A ARG* 3.6 41.3 - - + +
236A ARG* 3.8 15.0 - - + +
239A ALA* 4.4 0.4 - - + -
241A HIS* 4.4 8.5 - - + -
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Residues in contact with CYS 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 ALA 3.1 25.4 + - - +
72A ASN 3.5 2.0 - - - +
74A LEU* 1.3 77.8 - - - +
76A LEU* 1.3 63.8 + - - +
78A ALA* 3.3 7.4 + - - +
79A MET* 3.2 24.3 - - - +
177A HIS* 3.5 33.4 - - + -
205A ALA* 3.9 17.0 - - + -
206A LEU 4.3 7.0 - - - -
207A SER* 4.1 5.2 - - - -
221A ILE* 3.8 27.4 - - - -
223A LEU* 4.8 0.4 - - - -
232A MET* 4.0 7.6 - - - -
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Residues in contact with LEU 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 ASN 3.0 20.1 + - - +
73A ALA* 4.0 3.6 - - - +
75A CYS* 1.3 74.7 - - - +
77A SER* 1.3 63.8 + - - +
79A MET* 3.0 12.7 + - - +
80A THR* 3.0 25.1 + - - +
86A ILE* 4.0 28.3 - - + -
94A ILE* 3.9 37.2 - - + -
102A PRO* 4.2 13.0 - - + +
106A SER* 5.1 0.2 - - - -
144A CYS* 3.9 21.9 - - - -
146A SER* 4.2 4.9 - - - -
177A HIS* 3.9 32.8 - - + +
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Residues in contact with SER 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 ALA 2.9 16.5 + - - -
74A LEU* 2.7 24.3 + - - +
76A LEU* 1.3 75.5 - - - +
78A ALA* 1.3 59.1 + - - +
80A THR* 3.5 13.0 - - - +
105A PHE* 3.4 33.4 - - - +
106A SER* 3.8 13.3 - - - +
231A GLU* 3.9 0.2 - - - +
235A ARG* 3.2 38.7 + - - +
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Residues in contact with ALA 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 LEU 3.9 0.9 - - - +
75A CYS 3.3 5.2 + - - +
76A LEU 3.1 0.8 - - - -
77A SER* 1.3 79.9 + - - +
79A MET* 1.3 60.1 + - - +
80A THR 3.6 0.7 - - - -
228A LEU* 3.8 31.3 - - + +
231A GLU* 3.3 30.4 - - + +
232A MET* 3.8 28.0 - - + -
235A ARG* 3.9 5.2 - - - +
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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