Contacts of the helix formed by residues 61 - 70 (chain C) in PDB entry 2GVG
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 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C TYR* 1.3 81.1 - - - +
62C LEU* 1.3 65.1 + - - +
63C GLN 3.3 2.5 - - - -
64C TYR* 3.3 21.2 + - - +
65C ILE* 3.5 13.9 + - - +
121C GLU* 3.1 11.3 + - - -
155C SER* 4.9 1.8 - - - -
158C PRO* 3.8 17.8 - - - +
231C TYR* 3.4 10.1 - - - -
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Residues in contact with LEU 62 (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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59C PHE* 3.9 20.7 - - + -
60C TYR 3.8 1.4 + - - -
61C GLY* 1.3 76.0 - - - +
63C GLN* 1.3 56.4 + - - +
65C ILE* 2.8 31.3 + - + -
66C LEU* 2.9 36.5 + - + +
116C ILE* 4.2 11.0 - - + -
118C ALA* 4.1 17.7 - - + -
121C GLU* 2.9 9.2 + - - +
132C PHE* 4.5 15.0 - - + -
152C LEU* 3.9 21.1 - - + -
155C SER* 4.8 6.0 - - - -
461C VAL* 4.0 27.6 - - + -
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Residues in contact with GLN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLY 3.3 0.2 - - - -
62C LEU* 1.3 72.3 - - - +
64C TYR* 1.3 61.2 + - - +
66C LEU* 4.0 11.4 - - + +
67C ASN* 3.0 45.2 + - - +
121C GLU* 2.6 19.3 + - - +
230C TYR* 2.9 23.7 - - - +
231C TYR* 3.2 18.6 - - + -
467C VAL* 5.5 1.6 - - + -
469C LYS 4.2 3.1 + - - +
470C SER* 3.1 23.0 - - - +
471C TYR* 2.8 54.7 + - - +
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Residues in contact with TYR 64 (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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61C GLY* 3.3 11.6 + - - +
62C LEU 3.1 0.6 - - - -
63C GLN* 1.3 79.1 - - - +
65C ILE* 1.3 72.8 + - + +
68C LYS* 3.1 53.3 + - + +
69C TYR* 4.6 8.5 - + - -
158C PRO* 6.1 1.3 - - + -
202C GLU* 2.5 35.2 + - - +
206C ILE* 3.4 32.9 - - + +
226C LEU* 3.5 25.7 - - + +
230C TYR* 3.7 35.5 - + - -
231C TYR* 3.6 17.4 + - + +
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Residues in contact with ILE 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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61C GLY 3.6 11.0 - - - +
62C LEU* 2.8 13.8 + - + +
64C TYR* 1.3 87.0 - - + +
66C LEU* 1.3 64.0 + - - +
69C TYR* 3.0 38.2 + - + +
70C LEU* 3.5 10.3 + - + -
151C ILE* 3.7 32.5 - - + +
152C LEU* 4.2 20.6 - - + +
154C GLN* 4.5 3.8 - - + -
155C SER* 3.7 35.9 - - - +
158C PRO* 5.9 2.2 - - + -
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Residues in contact with LEU 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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62C LEU* 2.9 46.6 + - + +
63C GLN* 4.0 12.3 - - + +
65C ILE* 1.3 72.7 - - - +
67C ASN* 1.3 57.8 + - - +
70C LEU* 3.1 21.1 + - + -
71C LYS* 2.8 32.5 + - - +
116C ILE* 3.9 25.6 - - + -
461C VAL* 3.8 39.9 - - + +
462C PHE* 4.1 11.8 - - + -
467C VAL* 4.3 17.7 - - + -
469C LYS 5.5 0.4 - - - +
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Residues in contact with ASN 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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63C GLN* 3.0 38.0 + - - +
66C LEU* 1.3 81.7 - - - +
68C LYS* 1.3 60.6 + - - +
71C LYS* 3.0 57.2 + - - +
230C TYR* 3.8 25.1 + - + +
467C VAL* 3.6 21.5 - - - +
470C SER* 4.8 2.8 + - - -
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Residues in contact with LYS 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 PHE* 5.2 1.7 - - - +
64C TYR* 3.1 50.3 + - + +
67C ASN* 1.3 78.4 - - - +
69C TYR* 1.3 99.9 + - + +
202C GLU* 3.3 4.5 - - - -
229C LYS* 6.0 1.2 - - - +
230C TYR* 3.5 26.8 + - + +
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Residues in contact with TYR 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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201A GLN* 3.2 27.0 - - + +
9C PHE* 3.4 51.8 - + + -
11C ILE* 4.4 2.9 - - - +
64C TYR* 4.6 8.5 - + - -
65C ILE* 3.0 22.9 + - + +
68C LYS* 1.3 114.8 - - + +
70C LEU* 1.3 67.2 + - + +
71C LYS 3.7 1.1 - - - -
74C VAL* 3.5 19.1 - - - +
151C ILE* 3.6 31.6 - - + -
154C GLN* 5.6 1.1 - - - -
202C GLU* 2.5 29.2 + - - -
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Residues in contact with LEU 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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11C ILE* 4.0 19.1 - - + -
65C ILE* 3.5 12.1 + - + +
66C LEU* 3.1 25.1 + - + +
69C TYR* 1.3 85.4 - - + +
71C LYS* 1.3 64.2 + - - +
72C GLY 4.0 1.7 + - - +
74C VAL* 3.7 9.3 - - - +
112C LEU* 3.9 27.2 - - + +
116C ILE* 4.3 9.4 - - + -
148C ILE* 4.4 11.0 - - + -
151C ILE* 4.3 10.5 - - + -
152C LEU* 3.7 33.0 - - + -
462C PHE* 3.3 29.5 - - + -
465C GLY* 4.4 0.5 - - - -
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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