Contacts of the helix formed by residues 63 - 72 (chain C) in PDB entry 6H2V
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 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C VAL* 4.3 0.9 - - - -
60C CYS 2.9 16.4 + - - -
61C GLY 3.2 1.2 + - - -
62C CYS* 1.3 78.3 - - - +
64C VAL* 1.4 58.0 + - - +
65C LEU 3.4 2.5 - - - -
66C SER* 3.2 4.0 + - - -
67C ILE* 2.8 40.3 + - - +
90C PHE* 3.4 22.9 - - - -
301C SAM 3.9 0.2 + - - -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.4 36.1 - - + +
16C VAL* 3.8 27.6 - - + +
30C PRO* 3.8 7.2 - - + -
31C THR* 3.5 26.5 - - - +
33C PRO* 5.0 2.0 - - + -
36C ALA* 3.7 21.8 - - + -
40C LEU* 4.5 0.7 - - - +
62C CYS* 3.8 12.1 - - - -
63C GLY* 1.4 73.4 - - - +
65C LEU* 1.4 60.5 + - - +
67C ILE* 3.6 0.3 + - - +
68C GLY* 3.3 15.9 + - - -
301C SAM 3.3 20.8 + - - +
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C THR* 3.8 16.6 - - + +
36C ALA* 3.8 29.4 - - + -
39C MET* 4.0 23.3 - - + -
40C LEU* 3.7 16.3 - - + +
57C ASP* 3.8 13.4 + - - +
63C GLY 3.4 0.6 - - - -
64C VAL* 1.4 72.4 - - - +
66C SER* 1.3 55.4 + - - +
69C THR* 2.7 36.0 + - - -
124C ILE* 3.5 14.0 - - + +
125C MET* 3.9 34.3 - - - +
126C ASN* 3.9 13.7 - - + +
301C SAM 4.1 6.0 + - - +
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ASP* 2.7 37.3 + - - +
63C GLY 3.2 3.0 + - - -
65C LEU* 1.3 72.0 - - - +
67C ILE* 1.4 59.8 + - - +
69C THR* 3.5 1.6 - - - -
70C ALA* 2.9 29.8 + - - +
77C CYS* 3.3 22.5 - - - -
79C GLY* 4.1 4.2 - - - -
90C PHE* 3.3 33.2 - - - -
102C ILE* 4.2 4.1 - - - +
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.1 5.6 - - + -
16C VAL* 3.8 27.1 - - + -
63C GLY 2.8 30.2 + - - +
64C VAL 3.9 3.4 - - - +
66C SER* 1.4 69.1 - - - +
68C GLY* 1.3 58.3 + - - +
70C ALA 3.3 1.9 + - - -
71C MET* 3.0 33.7 + - - +
90C PHE* 4.5 6.3 - - + -
93C ASN* 3.8 15.3 - - + +
94C ALA* 3.5 38.4 - - + +
97C PHE* 3.8 24.9 - - + -
99C LEU* 3.3 18.6 - - + +
102C ILE* 4.0 7.4 - - + -
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.4 1.6 - - - -
13C LEU* 3.6 4.5 - - - +
40C LEU* 3.6 24.5 - - - -
64C VAL 3.3 7.7 + - - -
67C ILE* 1.3 77.0 - - - +
69C THR* 1.3 59.9 + - - +
71C MET* 3.4 21.2 + - - +
72C LEU* 3.2 29.5 + - - +
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.3 9.2 - - - +
50C ILE* 3.4 27.3 - - + +
55C VAL* 3.6 32.8 - - + -
65C LEU 2.7 23.3 + - - -
66C SER 3.3 5.8 + - - -
68C GLY* 1.3 71.9 - - - +
70C ALA* 1.3 64.8 + - - +
72C LEU 3.3 8.0 + - - -
74C ALA* 3.4 16.0 + - + +
77C CYS* 3.7 18.8 - - - -
124C ILE* 3.1 14.6 - - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER 2.9 16.7 + - - +
67C ILE 3.3 5.4 + - - +
69C THR* 1.3 76.0 - - - +
71C MET* 1.4 61.4 + - - +
72C LEU 3.4 0.9 + - - -
73C GLY* 3.4 8.1 + - - -
74C ALA* 4.6 2.2 - - - -
77C CYS* 4.7 1.5 - - + +
99C LEU* 3.8 9.7 - - + +
101C ASN* 3.1 45.8 + - - +
102C ILE* 3.6 23.6 - - + -
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Residues in contact with MET 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 4.3 13.5 - - + +
9C LEU* 3.6 22.4 - - + -
12C ARG* 3.3 61.5 + - + +
13C LEU* 3.7 15.3 - - + +
67C ILE* 3.0 15.6 + - - +
68C GLY* 3.6 26.0 - - - +
69C THR 3.3 0.4 - - - -
70C ALA* 1.4 74.3 - - - +
72C LEU* 1.4 56.6 + - - +
73C GLY 3.3 3.9 + - - -
97C PHE* 4.0 18.8 - - - -
99C LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 5.9 3.9 - - + +
4C VAL* 4.3 28.9 - - + +
9C LEU* 4.3 17.5 - - + -
40C LEU* 3.7 40.8 - - + +
41C TYR* 5.8 2.7 - - + -
44C HIS* 4.0 31.8 + - + -
45C ASN* 5.6 0.9 - - - +
50C ILE* 3.8 25.2 - - + +
51C GLU* 3.7 18.6 + - - +
68C GLY 3.2 20.9 + - - +
69C THR 3.3 0.4 + - - -
70C ALA 3.3 1.2 - - - -
71C MET* 1.4 74.7 - - - +
73C GLY* 1.3 60.2 + - - +
74C ALA 3.6 2.0 - - - -
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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