Contacts of the helix formed by residues 80 - 97 (chain D) in PDB entry 4QGC
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 THR 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D GLY* 1.3 75.5 - - - -
81D HIS* 1.3 65.1 + - - +
82D GLU* 3.3 18.6 + - - +
83D TYR* 3.1 24.0 + - + +
84D HIS* 3.1 27.8 + - - -
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Residues in contact with HIS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 3.9 16.5 - + - -
79D GLY 5.5 1.1 - - - -
80D THR* 1.3 76.3 - - - +
82D GLU* 1.3 57.8 + - + +
84D HIS* 4.7 1.1 - - - -
85D ALA* 2.9 32.1 + - - +
224D LYS* 6.2 0.4 - - - -
227D GLN* 3.5 33.4 - - + +
228D ASP* 2.6 29.5 + - - -
231D PHE* 3.3 37.5 - + + +
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D THR* 3.3 14.7 + - - +
81D HIS* 1.3 79.0 - - + +
83D TYR* 1.3 62.8 + - - +
85D ALA* 3.4 6.2 + - - +
86D GLU* 3.1 22.9 + - - +
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Residues in contact with TYR 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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51D ILE 5.9 0.9 - - - -
52D GLY* 5.4 3.6 - - - -
53D PRO* 3.6 31.6 - - + +
56D ARG* 3.3 51.4 + - - +
79D GLY* 4.6 8.5 - - - -
80D THR* 3.1 23.7 + - + +
82D GLU* 1.3 79.3 - - - +
84D HIS* 1.3 78.7 + + - +
86D GLU* 3.3 9.7 + - - +
87D THR* 3.1 29.6 + - - -
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Residues in contact with HIS 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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51D ILE 6.1 1.1 - - - -
74D LEU* 4.3 14.2 - - + +
75D ASN 3.3 23.6 + - - -
76D PHE* 3.6 46.8 - + + -
78D HIS 2.7 29.6 + - - -
79D GLY* 3.8 4.9 - - - -
80D THR 3.1 25.8 + - - +
81D HIS* 4.0 2.9 - + - +
83D TYR* 1.3 92.9 - + - +
85D ALA* 1.3 60.0 + - - +
87D THR* 3.2 7.8 + - - -
88D ILE* 2.9 35.8 + - - +
231D PHE* 4.4 2.5 - - + -
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Residues in contact with ALA 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 HIS 2.9 20.3 + - - +
82D GLU* 3.7 7.0 - - - +
83D TYR 3.3 0.2 - - - -
84D HIS* 1.3 77.7 - - - +
86D GLU* 1.3 61.4 + - - +
88D ILE* 3.6 3.2 + - - +
89D LYS* 3.1 22.3 + - - +
231D PHE* 3.6 19.5 - - + -
235D GLN* 4.2 16.9 - - - +
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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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56D ARG* 2.5 32.3 + - - +
82D GLU 3.1 13.3 + - - +
83D TYR* 3.5 9.9 - - - +
85D ALA* 1.3 75.4 - - - +
87D THR* 1.3 59.1 + - - +
89D LYS* 3.3 13.4 + - + +
90D ASN* 3.0 45.7 + - - +
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Residues in contact with THR 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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51D ILE* 3.6 33.7 - - + +
56D ARG* 3.2 30.5 - - + +
74D LEU* 3.6 23.3 - - + -
83D TYR* 3.1 20.6 + - - -
84D HIS* 3.2 11.5 + - - -
86D GLU* 1.3 75.1 - - - +
88D ILE* 1.3 59.1 + - - +
90D ASN* 3.1 4.8 + - - +
91D VAL* 2.9 36.4 + - + +
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Residues in contact with ILE 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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74D LEU* 3.5 31.9 - - + -
76D PHE* 5.6 0.7 - - + -
84D HIS 2.9 23.2 + - - +
85D ALA 3.8 4.7 - - - +
87D THR* 1.3 74.8 - - - +
89D LYS* 1.3 63.3 + - - +
91D VAL* 3.7 8.0 - - - +
92D ARG* 3.1 61.8 + - + +
110D VAL* 4.4 10.1 - - + -
112D LEU* 6.5 0.4 - - + -
231D PHE* 4.5 5.6 - - + -
235D GLN* 3.6 38.4 - - + +
237D VAL* 4.6 8.1 - - + -
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Residues in contact with LYS 89 (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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85D ALA 3.1 15.2 + - - +
86D GLU* 3.3 17.7 - - + +
87D THR 3.2 0.2 - - - -
88D ILE* 1.3 78.7 - - - +
90D ASN* 1.3 59.9 + - - +
92D ARG* 3.5 5.8 + - - +
93D THR* 2.7 44.7 + - - +
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Residues in contact with ASN 90 (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 ARG* 3.0 37.5 + - - +
57D SER* 4.6 3.6 - - - +
58D VAL* 3.8 23.8 - - + +
61D LEU* 3.6 6.4 - - + +
86D GLU* 3.0 34.9 + - - +
87D THR 3.1 6.0 + - - +
89D LYS* 1.3 84.2 + - - +
91D VAL* 1.3 59.5 + - - +
93D THR* 3.7 5.2 + - - -
94D ALA* 3.0 30.1 + - - +
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Residues in contact with VAL 91 (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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51D ILE* 4.5 2.0 - - + -
61D LEU* 3.7 29.6 - - + -
65D ILE* 4.6 1.0 - - + +
69D MET* 5.3 2.2 - - + -
72D ALA* 4.1 28.7 - - + -
74D LEU* 5.7 1.8 - - + -
87D THR* 2.9 31.6 + - + +
88D ILE* 3.7 7.9 - - - +
90D ASN* 1.3 75.3 - - - +
92D ARG* 1.3 56.5 + - + +
94D ALA* 3.4 3.1 + - - +
95D THR* 2.8 43.5 + - - +
108D VAL* 4.2 13.0 - - + +
110D VAL* 4.3 15.9 - - + -
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Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ILE* 3.1 40.9 + - + +
89D LYS* 3.9 4.9 - - - +
91D VAL* 1.3 75.1 - - + +
93D THR* 1.3 61.3 + - - +
95D THR* 4.2 6.7 - - - -
96D GLU* 3.0 39.7 + - + +
108D VAL 6.2 0.2 - - - +
110D VAL* 4.5 18.0 - - + +
235D GLN* 2.5 35.5 + - - +
236D ASP* 2.8 29.2 + - - +
237D VAL* 4.1 2.4 - - - +
238D ASP* 5.7 0.6 + - - -
461D ARG* 5.7 4.9 - - - +
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Residues in contact with THR 93 (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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58D VAL* 4.2 21.1 - - + -
62D LYS* 5.0 1.1 - - - -
89D LYS* 2.7 35.6 + - - +
90D ASN* 3.7 8.5 + - - -
92D ARG* 1.3 76.6 - - - +
94D ALA* 1.3 62.2 + - - +
96D GLU* 3.6 3.1 + - - +
97D SER* 3.3 22.6 + - - -
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Residues in contact with ALA 94 (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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58D VAL* 3.8 17.2 - - + +
61D LEU* 3.7 26.9 - - + -
62D LYS* 3.8 13.2 - - + +
65D ILE* 3.9 5.8 - - + -
90D ASN 3.0 17.4 + - - +
91D VAL 3.7 3.8 - - - +
93D THR* 1.3 76.1 - - - +
95D THR* 1.3 60.9 + - - +
97D SER* 2.6 24.9 + - - -
98D PHE* 3.1 12.6 - - - -
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Residues in contact with THR 95 (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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65D ILE* 3.5 13.2 - - - +
91D VAL* 2.8 24.8 + - - +
92D ARG* 3.9 8.2 - - - -
93D THR 3.3 0.2 - - - -
94D ALA* 1.3 77.5 - - - +
96D GLU* 1.3 76.6 + - - +
97D SER 3.2 1.2 + - - -
98D PHE* 3.3 16.0 + - - -
105D TYR* 3.4 25.1 - - + +
106D ARG 4.2 3.7 - - - +
108D VAL* 3.4 44.7 + - + +
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Residues in contact with GLU 96 (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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92D ARG* 3.0 25.9 + - + +
93D THR* 4.1 3.1 - - - +
95D THR* 1.3 83.9 - - - +
97D SER* 1.3 56.4 + - - +
98D PHE 3.0 5.4 - - - -
99D ALA* 3.1 37.0 + - + +
100D SER* 4.7 1.4 + - - -
105D TYR* 2.9 26.3 + - - -
475D LYS* 4.8 8.0 + - - -
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Residues in contact with SER 97 (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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62D LYS* 3.5 28.0 - - - +
93D THR* 3.3 14.5 + - - -
94D ALA 2.6 22.7 + - - -
95D THR 3.1 0.2 - - - -
96D GLU* 1.3 76.4 - - - +
98D PHE* 1.3 70.0 + - - +
99D ALA 3.5 0.2 - - - -
100D SER* 4.8 9.1 + - - -
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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