Contacts of the helix formed by residues 75 - 88 (chain D) in PDB entry 1C7G
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 GLU 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASN* 5.4 0.2 + - - -
41B LYS* 3.2 43.4 - - + +
68D ASP* 2.9 24.7 + - + +
73D GLY 3.5 0.6 + - - +
74D SER* 1.3 72.5 + - - +
76D ASN* 1.3 63.6 + - - +
78D TYR* 3.3 32.4 + - - +
79D HIS* 3.1 50.0 + - + -
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Residues in contact with ASN 76 (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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66D ILE* 3.6 18.4 + - - +
67D GLY* 4.2 0.6 - - - -
68D ASP* 2.5 38.6 + - - +
74D SER* 3.1 4.0 + - - +
75D GLU* 1.3 78.4 - - - +
77D PHE* 1.3 64.9 + - - +
79D HIS* 3.4 4.9 + - - +
80D LEU* 3.1 21.7 + - - +
296D GLY* 2.9 30.9 - - - +
299D MET* 3.8 9.4 - - + +
300D GLU* 2.6 43.5 + - - +
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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 GLY* 6.1 1.1 - - - -
74D SER* 3.2 15.3 + - - +
76D ASN* 1.3 76.1 - - - +
78D TYR* 1.3 82.3 + + - +
80D LEU* 3.2 4.7 + - + +
81D GLU* 2.8 67.4 + - + +
93D ILE* 4.5 13.5 - - + -
95D PRO* 3.8 28.3 - - + -
289D PRO 3.8 8.7 - - - -
290D SER* 3.7 32.3 - - - +
299D MET* 3.9 20.8 - - + -
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Residues in contact with TYR 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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37B LEU 5.1 1.7 + - - -
38B LEU 4.5 0.9 + - - -
39B ASN* 2.7 32.6 + - - -
73D GLY* 3.2 38.8 - - - -
74D SER 3.3 9.2 - - - -
75D GLU* 3.3 31.1 + - - +
77D PHE* 1.3 99.3 - + - +
79D HIS* 1.3 65.3 + - + +
81D GLU* 4.0 13.2 - - - +
82D LYS* 3.1 28.1 + - - +
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Residues in contact with HIS 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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66D ILE* 5.1 8.1 - - + -
75D GLU* 3.1 42.3 + - + -
76D ASN* 3.5 9.6 - - - +
78D TYR* 1.3 81.4 - - + +
80D LEU* 1.3 56.4 + - - +
82D LYS* 3.9 7.9 - - + +
83D THR* 2.9 32.6 + - - -
300D GLU* 2.6 38.9 + - - +
303D ALA* 4.0 9.2 - - + -
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Residues in contact with LEU 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 ASN 3.1 10.5 + - - +
77D PHE* 3.2 8.7 + - + +
79D HIS* 1.3 77.5 - - - +
81D GLU* 1.3 66.3 + - - +
83D THR* 3.1 2.5 + - - -
84D VAL* 2.9 42.3 + - + +
93D ILE* 3.9 18.6 - - + -
95D PRO* 4.4 13.5 - - + -
266D PHE* 4.8 3.4 - - + -
299D MET* 3.9 26.7 - - + +
302D MET* 3.8 35.7 - - + +
303D ALA* 3.7 28.9 - - - +
306D LEU* 5.4 1.8 - - + -
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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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77D PHE* 2.8 48.5 + - + +
78D TYR* 4.0 14.6 - - - +
80D LEU* 1.3 72.8 - - - +
82D LYS* 1.3 58.2 + - - +
84D VAL* 3.9 1.0 - - - +
85D LYS* 2.9 67.6 + - - +
92D HIS* 5.9 0.2 - - - -
93D ILE* 3.6 25.9 + - + +
275D PHE* 6.0 2.1 - - - -
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Residues in contact with LYS 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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78D TYR 3.1 17.7 + - - +
79D HIS* 3.9 8.5 - - + +
81D GLU* 1.3 82.6 + - - +
83D THR* 1.3 62.7 + - - +
85D LYS* 3.9 7.4 - - - +
86D GLU* 3.1 46.1 + - - +
307D ARG* 4.6 3.9 - - - +
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Residues in contact with THR 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 HIS 2.9 22.1 + - - -
80D LEU* 3.1 5.4 + - - -
82D LYS* 1.3 75.8 - - - +
84D VAL* 1.3 60.7 + - - +
86D GLU* 3.3 1.2 + - - +
87D LEU* 2.8 48.1 + - + +
303D ALA* 3.6 31.4 + - - +
306D LEU* 4.1 11.9 - - + -
307D ARG* 3.2 31.4 + - - +
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Residues in contact with VAL 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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80D LEU* 2.9 30.8 + - + +
81D GLU 4.0 1.3 - - - +
83D THR* 1.3 72.3 - - - +
85D LYS* 1.3 61.4 + - + +
87D LEU 4.5 0.4 - - - +
88D PHE* 2.7 49.8 + - + +
89D GLY 3.4 0.5 + - - -
90D PHE* 4.5 2.0 + - + -
93D ILE* 3.7 24.0 - - + -
266D PHE* 3.9 9.2 - - + -
268D CYS* 3.6 32.1 - - - -
306D LEU* 3.9 22.7 - - + -
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Residues in contact with LYS 85 (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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81D GLU* 2.9 54.5 + - - +
82D LYS* 3.9 7.9 - - - +
84D VAL* 1.3 76.6 - - + +
86D GLU* 1.3 59.6 + - - +
89D GLY* 2.9 28.4 + - - -
90D PHE 3.4 20.8 - - - +
91D LYS* 2.9 25.9 + - - +
92D HIS* 4.4 6.6 + - - +
93D ILE* 4.5 3.9 - - + +
242D HIS* 5.1 0.3 - - - -
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Residues in contact with GLU 86 (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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82D LYS* 3.1 34.1 + - - +
83D THR 3.7 2.2 - - - +
85D LYS* 1.3 82.4 - - - +
87D LEU* 1.3 69.9 + - + +
238D LYS* 4.4 13.6 + - - +
242D HIS* 3.7 15.9 + - - -
307D ARG* 3.1 37.2 + - - -
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Residues in contact with LEU 87 (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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83D THR* 2.8 42.1 + - + +
84D VAL* 4.9 0.7 - - - -
86D GLU* 1.3 89.4 - - + +
88D PHE* 1.3 73.2 + - + +
238D LYS* 3.8 34.3 - - + +
241D VAL* 4.0 6.2 - - + +
242D HIS* 3.5 24.1 + - - +
306D LEU* 3.8 21.5 - - + +
307D ARG* 4.2 19.1 - - + +
310D MET* 4.1 26.7 - - + -
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Residues in contact with PHE 88 (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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84D VAL* 2.7 34.5 + - + +
87D LEU* 1.3 84.0 - - + +
89D GLY* 1.3 57.7 + - - +
90D PHE* 3.4 17.3 + + + -
218D CYS* 4.0 15.5 - - - -
241D VAL* 4.0 10.1 - - + -
242D HIS* 4.4 7.8 + - - +
245D PHE* 3.3 63.7 - + + +
246D SER* 5.8 0.2 - - - -
251D CYS* 4.2 15.0 - - - -
253D MET* 4.0 17.5 - - + -
266D PHE* 3.8 25.8 - + - -
306D LEU* 4.0 22.9 - - + -
310D MET* 5.3 2.2 - - + -
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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