Contacts of the helix formed by residues 78 - 92 (chain D) in PDB entry 1USK
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 CYS 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D ILE* 3.3 20.2 - - - -
53D CYS* 2.1 50.7 - - + +
77D LEU* 1.3 87.7 - - - +
79D SER* 1.3 57.6 + - - +
80D SER* 3.5 7.9 - - - +
81D SER* 3.1 16.1 + - - +
82D THR* 2.6 29.3 + - - -
101D ALA* 4.2 1.6 - - - -
202D TYR* 3.9 9.2 - - + +
1347D LEU* 3.5 15.7 - - - +
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Residues in contact with SER 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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78D CYS* 1.3 75.4 - - - +
80D SER* 1.3 58.8 + - - +
82D THR* 3.4 0.9 + - - -
83D GLN* 3.2 27.0 + - - +
101D ALA* 3.6 9.9 - - - +
102D THR 3.3 3.6 + - - -
103D ASN* 3.1 39.6 + - - +
149D GLN* 3.7 11.8 + - - -
150D TYR* 4.5 10.9 - - - +
1347D LEU* 2.5 30.6 + - - -
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Residues in contact with SER 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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53D CYS 4.6 7.4 + - - -
55D PRO* 3.5 25.6 - - - +
78D CYS* 4.9 4.7 - - - +
79D SER* 1.3 78.7 + - - +
81D SER* 1.3 57.3 + - - +
84D PRO* 3.3 21.5 - - - +
148D GLN* 4.6 16.4 + - - +
149D GLN* 3.6 33.6 - - - +
150D TYR* 5.4 1.4 + - - +
202D TYR* 5.4 2.8 + - - -
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Residues in contact with SER 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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51D ASP* 3.3 24.0 + - - -
53D CYS* 4.0 23.5 - - - -
54D ASP 4.3 0.2 - - - -
55D PRO* 4.3 3.6 - - - -
58D ALA* 3.4 20.3 - - - +
76D HIS* 3.7 4.3 - - - +
78D CYS* 3.1 24.4 + - - +
80D SER* 1.3 80.3 + - - +
82D THR* 1.3 64.8 + - - +
83D GLN 3.4 0.4 - - - -
84D PRO* 3.6 2.2 - - - +
85D ALA* 3.3 22.5 + - - +
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Residues in contact with THR 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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76D HIS* 3.3 37.6 + - - +
78D CYS 2.6 22.3 + - - -
79D SER 3.4 3.3 + - - -
81D SER* 1.3 78.9 + - - +
83D GLN* 1.3 58.3 + - - +
85D ALA* 3.4 1.8 + - - +
86D SER* 2.9 27.2 + - - -
96D MET* 3.7 30.1 - - + +
98D SER* 4.0 9.0 - - - +
101D ALA* 3.8 7.4 - - + +
106D LEU* 4.0 15.0 - - + -
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Residues in contact with GLN 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 SER 3.2 13.9 + - - +
82D THR* 1.3 77.2 - - - +
84D PRO* 1.3 68.6 - - + +
86D SER* 2.6 22.5 + - - -
87D ASP* 3.4 11.6 + - - +
103D ASN* 4.3 2.0 + - - +
105D GLU* 2.9 39.4 + - - +
106D LEU* 4.3 16.1 - - + +
109D ARG* 3.5 32.0 + - - +
149D GLN* 2.6 36.3 + - - +
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Residues in contact with PRO 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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55D PRO* 4.4 17.0 - - + +
59D VAL* 3.9 19.4 - - + +
80D SER* 3.3 26.0 - - - +
81D SER* 3.6 8.3 - - - +
83D GLN* 1.3 94.7 - - + +
85D ALA* 1.3 60.9 + - - +
87D ASP* 3.5 26.3 + - - +
88D ILE* 3.9 12.1 + - - +
149D GLN* 5.7 0.7 - - - +
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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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58D ALA 4.0 10.1 - - - +
59D VAL* 4.7 1.0 - - - +
62D ALA* 4.0 9.9 - - + +
76D HIS* 3.2 38.8 - - + +
81D SER 3.3 15.9 + - - +
82D THR 3.4 2.4 + - - +
83D GLN 3.2 0.6 - - - -
84D PRO* 1.3 80.5 - - - +
86D SER* 1.3 61.2 + - - +
88D ILE* 3.3 7.2 + - - +
89D TYR* 3.2 28.5 + - + -
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Residues in contact with SER 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 THR 2.9 14.7 + - - -
83D GLN* 2.6 22.5 + - - -
85D ALA* 1.3 73.6 - - - +
87D ASP* 1.3 63.7 + - - +
89D TYR* 3.8 10.8 - - - +
90D GLU* 3.0 25.8 + - - +
96D MET* 4.2 3.1 - - - -
106D LEU* 3.7 12.3 - - - +
109D ARG* 3.1 19.8 + - - -
111D TYR* 3.8 3.5 - - - -
114D ILE* 3.8 24.3 - - - +
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Residues in contact with ASP 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 GLN* 3.5 12.7 - - - +
84D PRO* 3.6 15.8 - - - +
85D ALA 3.3 0.4 - - - -
86D SER* 1.3 77.4 + - - +
88D ILE* 1.3 62.2 + - + +
90D GLU* 3.6 3.1 + - - +
91D ASP* 3.3 29.2 + - - +
109D ARG* 3.2 20.6 + - - -
111D TYR* 2.8 30.5 + - - +
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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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59D VAL* 3.7 35.0 - - + +
62D ALA* 4.0 24.9 - - + +
63D ASN* 3.7 31.6 - - - +
66D VAL* 4.0 11.0 - - + -
84D PRO 3.9 12.3 + - - +
85D ALA 3.3 6.6 + - - +
86D SER 3.2 0.4 - - - -
87D ASP* 1.3 77.4 - - + +
89D TYR* 1.3 64.8 + - + +
90D GLU 3.2 0.2 - - - -
91D ASP* 3.4 8.4 + - - +
92D GLU* 3.2 28.4 + - + +
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Residues in contact with TYR 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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62D ALA* 3.5 31.9 - - + -
65D ILE* 3.3 28.4 - - + +
73D VAL* 4.0 18.2 - - + +
76D HIS* 3.0 33.0 + + - -
85D ALA* 3.2 17.6 + - + -
86D SER* 3.3 5.8 + - - +
88D ILE* 1.3 78.7 - - + +
90D GLU* 1.3 61.4 + - - +
92D GLU* 4.0 1.6 - - - -
93D GLY* 3.2 2.6 + - - -
94D ILE* 2.9 67.9 + - + +
96D MET* 3.6 35.2 - - + -
113D HIS* 4.6 0.6 - - - -
114D ILE* 4.6 5.6 - - + -
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Residues in contact with GLU 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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86D SER 3.0 15.7 + - - +
87D ASP 3.8 6.1 - - - +
89D TYR* 1.3 76.7 - - - +
91D ASP* 1.3 66.1 + - - +
92D GLU 3.4 0.2 + - - -
93D GLY* 3.5 9.0 + - - -
111D TYR* 3.4 49.4 - - + +
112D GLN* 3.2 12.2 + - - +
113D HIS* 2.7 47.7 + - - +
114D ILE* 3.6 6.6 - - - +
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Residues in contact with ASP 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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87D ASP* 3.3 16.5 + - - +
88D ILE* 3.4 11.9 + - - +
90D GLU* 1.3 80.7 - - - +
92D GLU* 1.3 71.1 + - + +
93D GLY 3.6 0.7 + - - -
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Residues in contact with GLU 92 (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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190B LYS 5.2 5.4 - - - +
193B ASN* 4.1 15.7 - - - +
66D VAL* 3.8 32.0 - - + +
88D ILE* 3.2 22.8 + - + +
89D TYR 4.6 0.2 - - - +
90D GLU 3.3 0.2 - - - -
91D ASP* 1.3 84.8 - - + +
93D GLY* 1.3 64.3 + - - +
94D ILE* 3.5 22.8 + - + +
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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