Contacts of the helix formed by residues 59 - 76 (chain D) in PDB entry 4GKH
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 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 1.3 75.1 - - - +
60D SER* 1.3 63.2 + - - -
62D ALA* 3.1 16.8 + - - +
63D ASN* 3.9 6.6 + - - -
89D ARG* 4.9 2.1 + - - -
92D ASP* 3.0 24.3 + - - +
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LYS 3.4 0.8 + - - -
59D GLY* 1.3 72.8 - - - -
61D VAL* 1.3 69.8 + - - +
63D ASN* 3.1 25.7 + - - +
64D ASP* 3.4 16.2 + - - +
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLY* 3.6 17.3 - - - +
38D ALA* 3.4 37.0 - - + +
57D GLY* 3.7 8.3 - - - -
58D LYS 3.1 18.0 + - - +
60D SER* 1.3 83.0 - - - +
62D ALA* 1.3 64.5 + - - +
64D ASP* 3.1 18.6 + - + +
65D VAL* 3.0 21.8 + - + +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLY* 3.3 26.3 - - - +
59D GLY 3.1 14.8 + - - +
61D VAL* 1.3 79.3 - - - +
63D ASN* 1.3 56.5 + - - +
65D VAL 3.3 0.7 + - - -
66D THR* 2.9 31.9 + - - -
89D ARG* 3.8 15.3 - - - +
92D ASP 3.8 11.0 - - - +
93D ASP 3.9 2.7 - - - -
94D ALA* 3.5 21.8 - - + +
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.0 21.2 + - - +
59D GLY 4.5 2.9 + - - -
60D SER* 3.1 22.4 + - - +
62D ALA* 1.3 73.9 - - - +
64D ASP* 1.3 63.8 + - - +
66D THR* 3.4 2.3 + - - -
67D ASP* 2.8 38.6 + - - +
89D ARG* 3.0 30.5 + - - +
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Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLY* 5.8 1.6 - - - -
60D SER* 3.5 12.6 + - - +
61D VAL* 3.1 27.3 + - + +
63D ASN* 1.3 79.4 - - - +
65D VAL* 1.3 62.0 + - + +
67D ASP* 3.3 13.4 + - - +
68D GLU* 3.1 21.1 + - - +
218D GLY* 5.0 2.4 - - - -
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA* 3.7 30.5 - - + -
55D LYS* 4.3 14.4 - - + +
57D GLY 3.9 10.8 - - - +
61D VAL* 3.0 20.1 + - + +
62D ALA 3.8 3.8 - - - +
64D ASP* 1.3 73.0 - - + +
66D THR* 1.3 59.5 + - - +
68D GLU* 3.2 8.4 + - - +
69D MSE 3.0 25.8 + - - +
87D PHE* 4.2 2.2 - - + -
94D ALA* 3.9 17.9 - - + -
96D LEU* 3.7 35.5 - - + +
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C MSE 3.9 22.0 - - + -
70C VAL* 3.6 25.6 - - + -
73C ASN* 5.0 7.0 - - - +
62D ALA 2.9 21.6 + - - -
63D ASN* 3.6 5.2 - - - -
65D VAL* 1.3 73.6 - - - +
67D ASP* 1.3 66.8 + - - +
69D MSE 3.2 10.4 + - + +
70D VAL* 3.2 15.0 + - - +
87D PHE* 3.7 15.9 - - + -
89D ARG* 2.9 30.2 + - - +
94D ALA* 4.0 0.2 - - - +
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Residues in contact with ASP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C VAL* 5.9 1.4 - - - +
63D ASN* 2.8 27.4 + - - +
64D ASP* 3.3 15.8 + - - +
66D THR* 1.3 73.9 - - - +
68D GLU* 1.3 61.0 + - - +
70D VAL* 3.4 2.7 - - - +
71D ARG* 3.1 54.8 + - - +
218D GLY* 3.8 13.8 - - - +
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Residues in contact with GLU 68 (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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55D LYS* 2.8 39.6 + - - +
64D ASP 3.1 10.1 + - - +
65D VAL* 3.6 8.5 - - - +
66D THR 3.2 0.4 - - - -
67D ASP* 1.3 77.4 - - - +
69D MSE 1.3 67.7 + - - +
71D ARG* 3.3 1.1 + - - +
72D LEU* 2.8 37.9 + - + +
82D PRO* 6.0 1.4 - - - +
96D LEU* 3.6 14.1 - - + +
216D ASP* 3.5 24.1 + - - +
217D VAL* 3.6 10.5 + - + +
218D GLY* 3.7 27.1 - - - +
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Residues in contact with MSE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR* 3.9 14.6 - - + -
69C MSE 3.4 33.7 - - + -
87C PHE* 4.0 1.8 - - + -
89C ARG* 4.7 10.8 - - - -
65D VAL 3.0 13.8 + - - +
66D THR 3.2 6.5 + - - +
68D GLU* 1.3 76.8 - - - +
70D VAL* 1.3 75.5 + - + +
72D LEU* 3.3 5.3 - - - +
73D ASN* 2.9 30.2 + - - +
84D ILE* 3.4 17.5 - - + +
87D PHE* 3.4 50.9 - - + -
96D LEU* 3.9 12.7 - - + +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR* 3.6 16.4 - - + -
67C ASP* 5.9 2.5 - - - +
70C VAL* 3.3 39.7 - - + -
141C PHE* 5.8 0.7 - - + -
66D THR 3.2 7.1 + - - +
67D ASP* 3.4 12.8 - - - +
69D MSE 1.3 93.2 - - + +
71D ARG* 1.3 79.2 + - - +
73D ASN* 3.4 6.1 + - - +
74D TRP* 3.1 28.1 + - - +
141D PHE* 3.6 18.1 - - + -
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Residues in contact with ARG 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C PRO* 4.0 23.6 + - - +
141C PHE* 5.3 3.4 - - - -
67D ASP* 3.1 47.8 + - - +
68D GLU 3.9 1.8 - - - +
70D VAL* 1.3 86.3 - - - +
72D LEU* 1.3 61.1 + - - +
74D TRP* 4.0 0.9 - - - +
75D LEU* 2.9 35.3 + - - +
141D PHE* 3.5 46.1 - - + +
142D ASN 5.4 2.2 + - - -
143D SER* 5.6 1.0 + - - -
147D PHE* 6.2 0.6 - - - -
148D ARG* 5.5 3.6 - - - +
217D VAL* 3.3 25.6 - - - +
218D GLY 3.2 24.7 + - - -
219D ARG* 4.3 1.0 - - - +
220D VAL* 3.0 29.7 + - + +
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Residues in contact with LEU 72 (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 GLU* 2.8 28.8 + - - +
69D MSE 3.3 4.7 - - - +
71D ARG* 1.3 76.3 - - - +
73D ASN* 1.3 62.4 + - - +
76D THR* 3.2 30.0 + - - -
81D LEU* 3.8 12.9 - - + +
82D PRO* 3.8 42.4 - - + +
84D ILE* 3.9 23.8 - - + -
96D LEU* 4.2 13.9 - - + -
98D THR* 4.0 19.5 - - + -
215D ILE* 6.1 0.2 - - - -
216D ASP 6.1 0.7 - - - +
217D VAL* 3.6 21.0 - - + +
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Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ASN* 2.8 34.5 + - - +
66C THR* 4.6 11.5 - - - +
67C ASP* 5.7 1.4 + - - -
89C ARG* 3.1 29.1 + - - +
69D MSE 2.9 21.6 + - - +
70D VAL* 3.6 9.6 + - - +
71D ARG 3.3 0.2 - - - -
72D LEU* 1.3 76.5 - - - +
74D TRP* 1.3 59.9 + - - +
76D THR* 3.4 17.1 - - - +
77D ALA* 5.5 0.9 - - - +
84D ILE* 4.1 14.3 - - + +
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Residues in contact with TRP 74 (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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70D VAL 3.1 16.8 + - - +
71D ARG 4.0 0.9 - - - +
73D ASN* 1.3 77.7 - - - +
75D LEU* 1.3 98.9 + - + +
76D THR 3.2 2.7 + - - -
77D ALA* 3.4 18.7 + - - +
78D PHE* 3.6 29.2 - + - -
134D ILE* 4.7 2.2 - - + -
138D ASN* 2.9 24.5 + - + -
139D CYS* 3.4 40.2 - - + -
140D PRO* 3.6 20.2 - - + -
141D PHE* 3.7 21.5 - + + -
194D VAL* 3.9 16.4 - - + -
220D VAL* 3.9 14.4 - - + -
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Residues in contact with LEU 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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71D ARG 2.9 21.3 + - - +
74D TRP* 1.3 95.6 - - + +
76D THR* 1.3 59.1 + - - +
77D ALA 3.0 3.1 - - - -
78D PHE* 2.8 23.4 + - + -
79D MSE 3.0 32.3 + - + +
81D LEU* 3.6 22.9 - - + -
131D LEU* 4.1 16.8 - - + -
134D ILE* 3.9 17.0 - - + -
194D VAL* 4.7 0.7 - - + -
196D HIS* 5.6 1.1 - - + -
214D CYS* 5.0 3.8 - - - -
217D VAL* 4.3 9.0 - - + -
220D VAL* 3.9 27.1 - - + -
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Residues in contact with THR 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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72D LEU 3.2 14.8 + - - +
73D ASN* 3.4 22.0 - - - +
75D LEU* 1.3 76.5 - - - +
77D ALA* 1.3 63.4 + - + +
78D PHE 3.1 0.9 + - - -
79D MSE 3.3 18.1 + - - +
81D LEU* 3.5 21.8 + - - +
82D PRO 4.9 4.3 + - - -
83D THR* 5.6 3.1 + - - -
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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
------------------------------------------------------------
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