Contacts of the helix formed by residues 74 - 84 (chain D) in PDB entry 2GER
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 ILE 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D PRO* 6.4 2.0 - - + -
70D VAL* 3.1 23.1 - - + -
71D LYS* 2.9 34.5 + - + +
73D HIS* 1.3 97.0 - - + +
75D ILE* 1.3 57.2 + - - +
76D PRO 3.1 2.2 - - - -
77D PHE* 2.5 43.2 + - + +
78D ILE* 3.2 29.3 + - + -
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 4.7 12.3 - - + +
70D VAL* 3.9 19.9 - - + +
71D LYS 3.5 2.4 + - - +
72D PRO 3.9 2.5 - - - +
74D ILE* 1.3 77.3 - - - +
76D PRO* 1.3 64.4 - - + +
77D PHE 2.6 13.2 + - - -
78D ILE* 4.4 9.0 - - - -
79D LEU* 2.6 54.9 + - + +
94D SER* 3.2 27.1 - - - +
96D ALA* 3.8 13.7 - - + -
99D VAL* 3.4 34.8 - - + -
104D ILE* 4.5 1.3 - - + -
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Residues in contact with PRO 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PRO 3.4 16.2 - - - +
73D HIS* 3.5 11.4 - - - +
74D ILE 3.3 2.9 - - - -
75D ILE* 1.3 97.9 - - + +
77D PHE* 1.3 74.6 + - + +
79D LEU* 4.2 5.1 - - + +
80D ASP* 3.2 17.7 + - - +
99D VAL* 5.4 1.3 - - + -
107D LYS* 3.5 17.6 + - - -
272D ALA* 4.9 14.4 - - + +
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Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D HIS 4.0 15.9 - - - -
74D ILE* 2.5 27.8 + - + +
76D PRO* 1.3 76.0 - - + +
78D ILE* 1.3 59.5 + - + +
79D LEU 3.1 1.1 - - - -
80D ASP* 2.5 40.8 + - - +
81D GLU* 3.6 4.0 + - - -
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.6 37.5 - - + -
35D PRO* 6.6 0.2 - - + -
56D ASN* 5.3 4.0 - - - +
68D LEU* 6.2 2.9 - - + -
70D VAL* 3.3 32.3 - - + -
74D ILE* 3.2 35.2 - - + +
75D ILE* 3.8 6.7 - - - +
77D PHE* 1.3 80.1 - - + +
79D LEU* 1.3 56.1 + - - +
80D ASP 2.6 21.8 + - - -
81D GLU* 3.3 17.4 + - - +
82D ILE* 3.3 20.2 + - + +
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 4.9 11.9 - - + -
75D ILE* 2.6 47.5 + - + +
76D PRO* 4.2 8.1 - - + +
78D ILE* 1.3 71.8 - - - +
80D ASP* 1.3 61.7 + - - +
82D ILE* 5.9 0.2 - - - -
83D GLY* 3.4 11.5 + - - -
92D VAL* 5.6 1.8 - - + -
103D SER 4.8 0.4 - - - +
104D ILE* 3.5 55.2 - - + +
107D LYS* 4.0 20.4 - - + +
108D LEU* 3.8 23.6 - - + +
111D PHE* 4.7 2.6 - - - -
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO 3.2 9.0 - - - +
77D PHE* 2.5 16.8 + - - +
78D ILE 2.6 0.2 + - - -
79D LEU* 1.3 68.2 - - - +
81D GLU* 1.3 54.0 - - - +
82D ILE 2.2 21.1 + - - -
83D GLY* 2.6 15.4 + - - -
84D ALA* 4.0 2.4 + - - +
107D LYS* 2.5 40.8 + - - +
111D PHE* 4.0 21.2 - - + -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASN* 3.7 34.5 + - - +
57D LYS* 3.7 20.3 + - - +
77D PHE 3.6 4.6 + - - +
78D ILE* 3.3 20.4 + - - +
80D ASP* 1.3 74.7 - - - +
82D ILE* 1.3 66.2 + - + +
84D ALA* 4.7 5.3 - - - +
85D ASP* 2.8 15.4 - - - +
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.9 16.8 - - + -
56D ASN* 3.8 29.8 - - + +
57D LYS* 4.2 2.0 - - + +
60D VAL* 3.4 42.6 - - + -
66D LEU* 5.6 2.2 - - + -
78D ILE* 3.3 12.7 + - + +
79D LEU* 5.9 0.2 - - - -
80D ASP 2.2 16.0 + - - -
81D GLU* 1.3 89.0 - - + +
83D GLY* 1.3 52.3 + - - +
84D ALA 2.5 7.8 + - - -
85D ASP* 2.4 39.7 + - + +
86D ILE* 2.9 8.1 + - + +
108D LEU* 5.1 0.2 - - - -
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Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU 3.4 6.1 + - - -
80D ASP 2.6 13.9 + - - -
82D ILE* 1.3 71.9 - - - +
84D ALA* 1.3 53.9 + - - +
86D ILE* 2.6 28.7 - - - +
108D LEU* 3.3 31.1 - - - +
111D PHE* 3.0 26.6 - - - +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LYS* 6.1 0.4 - - - +
80D ASP 5.0 0.9 - - - +
81D GLU 4.7 4.7 - - - +
82D ILE 2.5 4.8 + - - -
83D GLY* 1.3 76.1 - - - +
85D ASP* 1.3 68.9 + - - +
86D ILE 3.2 7.7 + - - +
111D PHE* 3.1 26.9 - - + -
112D ARG* 5.8 0.2 + - - -
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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