Contacts of the strand formed by residues 86 - 98 (chain C) in PDB entry 1QD6
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 SER 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.4 9.1 - - - +
80C GLY 3.0 21.1 + - - -
81C ILE* 3.6 4.3 + - - +
82C LEU* 2.8 34.3 + - - -
83C GLY 3.0 10.7 + - - -
85C ASN* 1.3 76.9 - - - +
87C VAL* 1.3 65.9 + - - +
120C LEU* 6.2 0.2 - - - -
121C GLY 3.0 8.1 - - - -
122C PHE* 3.4 33.2 - - - -
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.8 28.5 - - + -
22A MET* 4.7 16.2 - - + -
23A LEU* 4.3 7.4 - - + -
76C PRO* 4.1 24.9 - - + -
78C TRP 3.3 15.0 - - - +
79C ARG* 4.2 6.7 - - + -
81C ILE* 4.1 4.5 - - - -
86C SER* 1.3 78.2 - - - +
88C LEU* 1.3 75.7 + - - +
89C GLY* 3.6 1.8 + - - +
119C PHE* 4.9 2.0 - - + -
120C LEU* 3.5 2.8 - - - +
121C GLY* 2.8 49.0 + - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 2.9 34.3 + - + -
78C TRP* 2.9 38.8 + - + +
81C ILE* 3.7 26.7 - - + +
87C VAL* 1.3 75.4 - - - +
89C GLY* 1.3 63.0 + - - +
118C LEU* 3.9 25.6 - - + -
119C PHE 3.5 13.7 - - - +
120C LEU* 4.2 9.9 - - + -
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Residues in contact with GLY 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A MET* 5.1 0.4 - - - -
75C PHE 3.5 10.8 - - - -
76C PRO* 4.5 2.9 - - - -
77C LEU* 3.9 6.1 - - - -
87C VAL* 3.6 4.0 + - - -
88C LEU* 1.3 76.5 - - - +
90C ALA* 1.3 61.6 + - - -
118C LEU* 3.5 8.8 - - - +
119C PHE* 2.9 51.0 + - - +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ALA* 3.4 3.1 - - - -
75C PHE* 2.6 52.8 + - + +
77C LEU* 4.0 16.4 - - + -
89C GLY* 1.3 74.6 - - - +
91C SER* 1.3 58.8 + - - +
117C GLN 3.3 13.9 - - - +
118C LEU* 4.6 4.9 - - + -
119C PHE* 3.7 7.8 - - - -
270C HDS 6.5 0.4 - - + -
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.6 30.1 - - - -
73C LEU 3.1 14.1 - - - -
74C ALA* 4.3 0.2 - - - -
75C PHE* 4.0 4.5 - - - -
90C ALA* 1.3 77.6 - - - +
92C TYR* 1.3 65.6 + - - +
93C THR* 5.2 0.3 + - - -
115C GLU 4.9 0.9 + - - -
116C PRO* 3.4 3.1 - - - +
117C GLN* 3.0 60.0 + - - +
119C PHE* 3.8 3.6 - - - -
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.7 4.4 - - + +
72C SER* 3.2 2.8 - - - -
73C LEU* 2.9 34.1 + - + -
75C PHE* 3.9 18.6 - + + -
91C SER* 1.3 77.7 - - - +
93C THR* 1.3 62.9 + - - +
94C GLN* 2.7 42.7 + - + -
114C TYR* 3.2 23.3 - - + -
115C GLU 3.6 17.7 - - - -
116C PRO* 4.1 11.7 - - + -
270C HDS 3.7 41.5 - - + -
69D PHE* 3.9 6.7 - + - -
71D LEU* 3.6 33.2 - - + -
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 4.1 12.8 - - - -
36C ASP* 4.1 6.5 + - - +
70C GLN* 3.8 29.6 - - + +
71C LEU 3.3 7.6 - - - +
72C SER* 2.9 21.8 + - - -
91C SER* 5.2 0.7 + - - -
92C TYR* 1.3 73.9 - - - +
94C GLN* 1.3 64.4 + - - +
95C LYS* 3.9 13.5 - - + +
113C ASN 3.8 0.9 - - - +
114C TYR* 3.7 0.3 - - - -
115C GLU* 2.7 58.0 + - - +
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.7 6.4 - - - +
70C GLN* 3.1 7.3 - - - +
71C LEU* 2.8 53.8 + - + +
92C TYR* 2.7 37.2 + - + +
93C THR* 1.3 74.3 - - - +
95C LYS* 1.3 63.6 + - - +
96C SER* 3.4 17.9 + - - +
112C THR* 3.6 22.9 - - + +
113C ASN 3.2 5.8 - - - +
114C TYR* 4.0 2.1 - - + -
71D LEU* 3.9 2.9 - - - +
94D GLN* 2.8 42.7 + - - -
114D TYR* 5.1 2.0 - - - -
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Residues in contact with LYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ASP* 4.5 1.4 + - - -
39C TYR* 5.5 1.8 - - - +
68C LYS* 5.4 8.1 - - + -
69C PHE 3.4 6.3 - - - +
70C GLN* 2.6 36.2 + - + +
93C THR* 3.9 12.9 - - + +
94C GLN* 1.3 76.6 - - - +
96C SER* 1.3 61.6 + - - +
97C TRP* 3.5 32.1 - - + -
112C THR* 3.2 4.2 - - - +
113C ASN* 2.7 48.3 + - + +
115C GLU* 4.3 15.7 + - - -
211C LYS* 3.8 17.5 - - - +
247C GLU 4.7 7.2 - - - +
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Residues in contact with SER 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL 3.6 0.7 - - - +
68C LYS* 3.3 7.3 - - - +
69C PHE* 2.9 45.4 + - - -
94C GLN* 3.4 14.9 + - - -
95C LYS* 1.3 71.6 - - - +
97C TRP* 1.3 67.5 + - - +
98C TRP 4.1 0.4 - - - -
109C PHE* 3.4 27.4 - - - -
111C GLU 3.4 4.0 - - - -
112C THR* 3.3 25.2 + - - +
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Residues in contact with TRP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 3.5 21.3 - - + +
67C VAL 3.4 4.9 - - - -
68C LYS* 3.4 39.3 - - + +
95C LYS* 3.5 37.2 - - + -
96C SER* 1.3 74.0 - - - +
98C TRP* 1.3 54.8 + - - +
109C PHE* 3.6 4.4 - - - +
110C ARG* 2.8 56.4 + - - +
111C GLU* 2.8 34.9 + - + +
113C ASN* 3.9 10.1 - - - -
247C GLU* 3.1 43.1 + - - -
248C SER* 3.4 25.1 - - - -
258C ARG* 3.8 10.5 - - - -
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Residues in contact with TRP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 6.1 0.7 - - + -
66C GLU* 3.5 4.0 - - - +
67C VAL* 2.8 63.1 + - + +
69C PHE* 5.1 3.4 - + + -
97C TRP* 1.3 73.6 - - - +
99C GLN* 1.3 56.0 + - - +
100C LEU* 2.8 54.4 + - + -
107C SER* 3.0 34.9 + - - -
108C PRO 3.7 2.5 - - - -
109C PHE* 3.6 28.9 - + + +
116D PRO* 6.2 0.4 - - + -
142D HIS* 5.5 3.6 - + - -
270D HDS 3.4 69.6 + - + +
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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