Contacts of the helix formed by residues 72 - 83 (chain A) in PDB entry 2GP0
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 SER 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO 3.6 2.9 + - - -
71A PRO* 1.3 75.2 - - - +
73A PRO* 1.4 76.0 - - - +
74A LYS* 3.6 8.0 + - - +
75A GLN* 3.0 39.3 + - - +
76A LEU* 2.9 20.7 + - - +
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Residues in contact with PRO 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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71A PRO 4.5 1.3 - - - +
72A SER* 1.4 84.7 - - - +
74A LYS* 1.3 62.1 + - - +
76A LEU* 3.3 4.0 + - + -
77A GLU* 3.0 26.0 + - - +
320A GLN* 3.0 28.1 + - + +
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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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72A SER* 3.2 7.4 + - - +
73A PRO* 1.3 77.7 - - - +
75A GLN* 1.3 65.0 + - + +
77A GLU* 3.3 21.9 + - - +
78A GLU* 3.1 57.7 + - + +
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Residues in contact with GLN 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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59A HIS* 6.4 0.2 - - + -
70A PRO 5.0 0.2 - - - +
71A PRO* 3.5 15.1 - - + +
72A SER* 3.0 41.4 + - - +
74A LYS* 1.3 76.5 - - + +
76A LEU* 1.3 58.4 + - - +
78A GLU* 3.4 10.6 + - - +
79A GLU* 2.9 31.2 + - - +
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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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70A PRO* 5.9 0.7 - - + -
71A PRO* 3.6 36.3 - - + +
72A SER 2.9 19.0 + - - +
73A PRO* 3.8 4.5 - - + +
75A GLN* 1.3 74.6 - - - +
77A GLU* 1.3 59.2 + - - +
79A GLU* 3.7 9.9 - - - +
80A PHE* 2.9 31.9 + - - +
316A ALA* 5.5 0.4 - - - -
319A TYR* 3.7 12.8 - - + -
320A GLN* 3.9 28.7 - - + +
323A HIS* 3.4 52.3 - - + +
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Residues in contact with GLU 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 PRO* 3.0 22.3 + - - +
74A LYS* 3.3 25.9 + - - +
76A LEU* 1.3 77.2 - - - +
78A GLU* 1.3 63.5 + - + +
80A PHE* 3.8 1.6 - - - +
81A LEU* 3.1 34.7 + - + +
316A ALA* 4.2 22.2 - - + +
320A GLN* 3.6 16.6 + - - +
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Residues in contact with GLU 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 LYS* 3.1 54.8 + - - +
75A GLN* 4.0 7.6 - - - +
77A GLU* 1.3 72.9 - - + +
79A GLU* 1.3 66.1 + - - +
81A LEU* 3.4 12.5 + - + +
82A LYS* 3.2 41.2 + - - +
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Residues in contact with GLU 79 (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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53A PHE* 5.5 0.3 - - - -
59A HIS* 2.8 34.3 + - - +
71A PRO* 5.8 0.2 - - - +
75A GLN 2.9 19.5 + - - +
76A LEU* 3.7 15.5 - - - +
78A GLU* 1.3 77.2 - - - +
80A PHE* 1.3 64.3 + - - +
82A LYS* 3.1 25.2 + - - +
83A ILE* 3.4 10.4 - - - +
299A LEU* 3.8 28.5 + - + +
319A TYR* 2.5 33.4 + - + +
323A HIS* 4.7 2.8 + - - -
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Residues in contact with PHE 80 (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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76A LEU 2.9 20.0 + - - +
77A GLU 3.8 3.8 - - - +
78A GLU 3.4 0.2 - - - -
79A GLU* 1.3 76.9 - - - +
81A LEU* 1.3 70.5 - - + +
83A ILE* 3.1 32.5 + - + +
302A VAL* 5.0 1.3 - - + -
306A ARG* 3.5 21.8 + - - -
313A ILE* 3.4 39.0 - - + -
314A GLN 3.6 15.3 - - - -
315A THR 3.5 8.5 - - - -
316A ALA* 3.5 34.1 - - + -
319A TYR* 3.5 30.2 - + + -
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Residues in contact with LEU 81 (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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77A GLU* 3.1 27.1 + - + +
78A GLU* 3.8 11.4 - - + +
79A GLU 3.3 0.2 - - - -
80A PHE* 1.3 84.7 - - + +
82A LYS* 1.3 61.5 + - + +
83A ILE 3.3 5.6 + - - +
316A ALA* 6.0 2.0 - - + -
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Residues in contact with LYS 82 (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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53A PHE* 3.8 24.7 - - + -
78A GLU* 3.2 30.5 + - - +
79A GLU* 3.1 14.7 + - - +
81A LEU* 1.3 74.7 - - + +
83A ILE* 1.3 63.0 + - - +
84A PRO* 3.2 10.9 - - - +
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Residues in contact with ILE 83 (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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53A PHE* 4.0 3.8 - - + -
54A LEU* 3.8 13.2 - - + -
79A GLU 3.4 11.9 - - - +
80A PHE* 3.1 29.1 + - + +
81A LEU 4.1 4.9 - - - +
82A LYS* 1.3 76.0 - - - +
84A PRO* 1.3 78.0 - - + +
85A SER 3.7 0.9 + - - -
299A LEU* 3.6 28.9 - - + -
302A VAL* 4.0 24.9 - - + -
303A CYS* 4.2 9.4 - - - -
306A ARG* 3.2 29.9 + - + +
319A TYR* 4.2 13.9 - - + -
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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