Contacts of the strand formed by residues 78 - 90 (chain D) in PDB entry 3QS1
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 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D MET 3.7 0.2 - - - +
75D TYR* 2.5 40.5 + - - +
76D VAL 3.2 3.0 + - - -
77D SER* 1.3 80.5 - - - +
79D THR* 1.3 62.9 + - - -
109D GLY* 3.5 22.2 - - - -
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Residues in contact with THR 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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72D GLU* 4.7 8.5 - - + -
73D MET 2.9 22.7 - - - +
74D ASN* 2.8 34.4 + - - +
75D TYR* 4.1 1.8 + - - -
78D GLY* 1.3 77.0 + - - -
80D VAL* 1.3 74.2 + - - +
81D SER* 5.5 0.4 - - - +
106D ASP 4.3 1.7 - - - +
109D GLY* 3.1 38.8 + - - +
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Residues in contact with VAL 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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39D TRP* 4.6 18.8 - - + +
71D VAL 4.8 0.2 - - - -
72D GLU* 3.9 3.5 - - - -
73D MET* 3.0 55.5 + - + +
75D TYR* 4.8 8.3 - - + -
79D THR* 1.3 85.8 - - - +
81D SER* 1.3 69.1 + - - +
102D ILE* 6.1 2.0 - - + -
104D VAL* 4.3 23.8 - - + -
106D ASP 3.6 9.2 - - - +
107D THR* 4.6 5.2 - - + -
109D PHE* 4.0 26.7 - - + +
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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
----------------------------------------------------------
71D VAL 3.9 4.9 - - - -
72D GLU* 4.4 15.8 + - - +
79D THR* 5.5 1.0 - - - +
80D VAL* 1.3 79.6 + - - +
82D GLY* 1.3 52.5 + - - +
102D ILE* 5.2 2.9 - - - -
104D VAL* 3.5 5.2 - - - -
105D THR* 2.6 32.9 + - - -
106D ASP* 2.8 44.0 + - - -
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Residues in contact with GLY 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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70D LYS* 3.4 12.6 + - - +
71D VAL 3.1 26.8 + - - +
72D GLU* 5.4 0.3 - - - +
81D SER* 1.3 75.7 - - - +
83D PHE* 1.3 65.4 + - - +
102D ILE* 4.5 4.5 - - - +
103D GLU 3.1 14.1 - - - -
105D THR* 3.7 11.4 - - - -
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Residues in contact with PHE 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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42D SER* 4.0 7.2 - - - -
44D GLN* 4.5 15.3 - - + -
58D SER* 6.0 0.4 - - - -
64D TYR* 5.1 6.5 - - - -
66D LYS* 6.0 2.0 - - - -
68D GLY* 3.3 22.2 - - - +
69D THR 2.9 16.6 - - - +
70D LYS* 3.8 6.7 - - + +
71D VAL* 4.3 2.0 - - - +
82D GLY* 1.3 78.0 - - - +
84D PHE* 1.3 75.5 + - - +
85D SER* 3.3 18.4 - - - -
102D ILE* 4.1 5.9 - - - +
103D GLU* 2.8 57.5 + - + -
105D THR* 3.6 26.7 - - + -
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Residues in contact with PHE 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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64D TYR* 5.4 0.2 + - - -
67D ASP* 3.7 23.8 - - - +
68D GLY 3.1 19.4 + - - -
69D THR* 2.6 32.0 + - + +
70D LYS 5.0 0.2 - - - -
71D VAL* 3.4 27.6 - - + -
83D PHE* 1.3 76.6 - - - +
85D SER* 1.3 68.4 + - - +
100D LYS* 3.4 34.5 - - + -
101D PHE 3.3 15.5 - - - -
102D ILE* 3.7 22.2 - - + -
130D ILE 3.2 25.4 - - - -
131D GLY* 4.0 13.9 - - - -
133D VAL* 4.2 5.4 - - + -
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Residues in contact with SER 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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64D TYR* 4.0 12.7 + - - -
65D GLU 4.2 0.4 - - - -
67D ASP* 3.9 14.1 - - - +
83D PHE* 3.3 5.7 - - - -
84D PHE* 1.3 82.0 + - - +
86D LYS* 1.3 62.4 + - - +
100D LYS* 3.3 12.3 - - - +
101D PHE* 2.7 47.9 + - - -
103D GLU* 2.9 33.6 + - - +
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Residues in contact with LYS 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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64D TYR* 3.4 7.4 - - - -
65D GLU* 3.1 76.1 + - + +
66D LYS 5.6 0.4 - - - +
67D ASP* 5.6 2.2 - - + -
85D SER* 1.3 72.7 - - - +
87D ASP* 1.3 68.5 + - - +
98D PRO* 3.4 32.5 - - - +
99D TYR 3.0 26.3 - - - +
100D LYS* 3.5 21.3 - - + -
101D PHE* 3.6 3.5 - - - -
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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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20D ILE* 3.2 22.0 - - + -
21D GLY* 3.2 17.9 - - - -
56D TYR* 2.2 29.7 + - - +
61D SER* 3.2 14.4 + - - -
63D THR* 3.6 12.7 - - - -
64D TYR* 3.0 22.6 + - - +
65D GLU* 5.5 0.2 - - - -
86D LYS* 1.3 79.3 - - - +
88D ILE* 1.3 76.1 + - - +
89D VAL* 3.4 4.5 + - - +
98D PRO* 3.5 4.4 - - - +
99D TYR 3.0 30.6 + - - +
101D PHE* 3.5 4.5 - - + -
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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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20D ILE* 3.6 2.4 - - - -
21D GLY 3.0 27.5 + - - +
22D ASP* 3.8 17.9 - - + +
24D LYS* 6.4 0.7 - - - -
63D THR* 3.8 29.7 - - + +
87D ASP* 1.3 91.8 + - - +
89D VAL* 1.3 62.7 + - - +
90D THR* 3.8 4.7 + - - +
95D SER* 3.9 20.2 - - - -
96D PHE* 3.5 28.5 - - - +
98D PRO* 4.5 3.8 - - + -
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Residues in contact with VAL 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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18D ALA* 5.9 0.4 - - + -
19D GLN 3.6 8.7 - - - +
20D ILE* 3.8 21.5 - - + -
29D PHE* 6.4 2.0 - - + -
38D LEU* 4.5 19.1 - - + -
87D ASP 4.0 3.1 - - - +
88D ILE* 1.3 71.7 - - - +
90D THR* 1.3 61.6 + - - +
91D ILE* 3.5 26.2 - - + -
95D SER* 3.2 1.7 - - - -
96D PHE* 2.9 49.6 + - + +
99D TYR* 3.5 28.5 - - + -
101D PHE* 4.6 10.1 - - + -
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Residues in contact with THR 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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18D ALA* 3.5 5.7 - - - +
19D GLN* 2.6 54.3 + - - +
21D GLY 4.9 0.7 + - - -
24D LYS* 3.6 24.6 - - - +
88D ILE* 4.0 6.4 + - - +
89D VAL* 1.3 75.3 - - - +
91D ILE* 1.3 61.5 + - - +
92D ALA 3.6 11.2 - - - +
93D ASN* 3.8 3.1 - - - -
94D LEU 2.9 23.6 - - - +
95D SER* 3.0 29.1 + - - +
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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