Contacts of the strand formed by residues 109 - 128 (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 PHE 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TYR* 5.5 0.2 - - - -
58C TRP* 4.0 8.5 + - - -
69C PHE* 3.8 11.2 - + - -
96C SER* 3.4 28.5 - - - -
97C TRP 3.6 9.6 - - - +
98C TRP* 3.6 21.3 - + + +
108C PRO* 1.3 74.6 - - - +
110C ARG* 1.3 62.1 + - - +
111C GLU 4.5 2.7 - - - +
112C THR* 3.6 20.2 - - - +
147C ARG* 3.3 17.1 + - - +
114D TYR* 3.4 42.2 - + - +
146D GLY* 2.9 26.9 + - - +
270D HDS 3.5 36.8 - - + -
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.6 30.9 - - - +
49C ASN* 5.3 4.8 + - - +
53C ILE* 3.5 33.4 - - + +
56C TYR* 3.9 3.6 - - - -
58C TRP* 3.9 22.2 - - + -
62C ALA* 5.7 0.2 - - - -
66C GLU* 2.7 46.4 + - - +
97C TRP* 2.8 37.3 + - - +
99C GLN* 4.2 2.7 - - + +
108C PRO 3.5 3.2 + - - -
109C PHE* 1.3 73.5 - - - +
111C GLU* 1.3 64.9 + - - +
147C ARG* 3.4 12.9 + - - -
247C GLU* 4.7 1.0 + - - -
248C SER* 4.3 2.4 + - - -
250C ILE* 3.8 14.3 - - - +
251C ASP* 3.0 31.7 + - - -
258C ARG* 3.6 9.9 - - - +
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ILE* 5.3 0.5 - - - +
56C TYR* 5.3 1.0 + - - -
96C SER* 4.1 0.2 - - - -
97C TRP* 2.8 52.0 + - + +
109C PHE* 3.4 2.4 - - - -
110C ARG* 1.3 93.0 - - + +
112C THR* 1.3 67.1 + - - +
113C ASN* 2.7 30.7 + - - +
145C ASN* 3.3 26.4 + - - +
147C ARG* 4.4 10.0 + - - +
248C SER* 3.9 8.5 - - - -
249C LEU 3.5 0.5 + - - -
250C ILE* 3.1 43.3 + - + +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 3.6 15.0 - - + +
95C LYS 3.2 7.2 - - - +
96C SER* 3.3 23.9 + - - +
109C PHE* 3.6 15.2 - - - +
111C GLU* 1.3 75.6 + - - +
113C ASN* 1.3 73.2 + - - +
114C TYR* 3.3 42.3 + - + +
145C ASN* 3.1 26.6 + - - +
147C ARG* 5.1 3.7 + - - +
114D TYR* 4.3 5.5 + - + +
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Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR 3.8 0.9 - - - +
94C GLN* 3.2 8.5 - - - +
95C LYS* 2.7 48.9 + - + +
97C TRP* 3.9 11.3 - - + -
111C GLU* 2.7 28.7 + - - -
112C THR* 1.3 78.4 + - - +
114C TYR* 1.3 62.0 + - - +
115C GLU* 5.3 1.1 - - + +
143C ASP* 3.9 13.2 - - - +
144C SER 3.4 2.2 - - - +
145C ASN* 3.7 7.1 - - - +
247C GLU 4.6 0.5 - - - +
248C SER* 3.3 11.8 - - - -
249C LEU* 3.0 33.6 + - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 3.2 28.0 - - + +
93C THR 3.9 2.0 - - - -
94C GLN* 4.0 5.8 - - + -
112C THR* 3.3 37.1 + - + +
113C ASN* 1.3 70.5 - - - +
115C GLU* 1.3 60.1 + - - +
116C PRO* 3.4 9.8 - - - +
142C HIS 3.5 0.7 - - - +
143C ASP* 3.5 0.8 - - - -
144C SER 2.8 39.3 + - - +
145C ASN 3.4 27.5 + - - -
146C GLY* 3.8 5.4 - - - -
270C HDS 3.5 32.5 + - + -
69D PHE* 4.7 2.0 - + - -
94D GLN* 5.0 3.1 - - - -
96D SER* 5.1 0.2 - - - -
109D PHE* 3.5 41.6 - + - +
112D THR* 4.4 6.6 + - + +
114D TYR* 5.0 3.1 + - - -
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER* 4.9 0.3 + - - -
92C TYR* 3.6 4.4 + - - -
93C THR* 2.7 46.7 + - - +
95C LYS* 4.3 22.5 + - - -
113C ASN* 5.3 1.3 - - - +
114C TYR* 1.3 73.4 - - - +
116C PRO* 1.3 60.6 - - - +
117C GLN* 4.0 6.6 + - + +
141C ASN* 2.8 33.3 + - - +
142C HIS 3.2 7.4 - - - +
143C ASP* 3.8 16.7 - - - +
157C ARG* 3.5 15.3 + - - -
174C LYS* 4.4 8.1 + - - -
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Residues in contact with PRO 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER 3.4 9.6 - - - +
92C TYR* 4.1 5.6 - - + -
114C TYR 3.4 7.2 - - - +
115C GLU* 1.3 89.5 - - - +
117C GLN* 1.3 62.2 + - - +
140C TYR* 5.6 1.2 - - - -
141C ASN* 3.7 0.3 - - - -
142C HIS* 3.1 52.2 + - + +
270C HDS 4.0 37.9 - - + -
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Residues in contact with GLN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.0 33.2 + - - -
90C ALA* 3.3 9.8 - - - +
91C SER* 3.0 47.9 + - - +
115C GLU* 4.4 5.6 - - + +
116C PRO* 1.3 75.1 - - - +
118C LEU* 1.3 60.4 + - - +
119C PHE* 4.3 3.1 - - + -
137C GLU* 3.8 0.4 + - - -
140C TYR* 3.2 11.4 - - - +
141C ASN* 2.8 27.0 + - + +
159C TYR* 3.3 24.4 + - - +
174C LYS* 2.8 26.6 + - - -
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.2 13.9 - - + -
88C LEU* 3.9 19.3 - - + -
89C GLY 3.5 17.0 - - - +
90C ALA* 4.6 4.0 - - + -
117C GLN* 1.3 74.2 - - - +
119C PHE* 1.3 62.6 + - - +
139C GLY* 3.0 2.3 - - - -
140C TYR* 2.8 46.3 + - + +
159C TYR* 4.4 0.2 + - - -
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.1 9.0 - - + -
22A MET* 3.6 33.9 - - + -
35C TYR* 4.0 9.6 - + - -
87C VAL* 4.9 2.5 - - + -
88C LEU* 3.5 9.3 - - - +
89C GLY* 2.9 51.3 + - - +
90C ALA 3.7 26.5 - - - -
91C SER* 3.8 12.6 - - - -
117C GLN* 4.3 7.0 - - + -
118C LEU* 1.3 79.7 - - - +
120C LEU* 1.3 61.8 + - - +
121C GLY* 4.0 6.7 - - - -
137C GLU* 3.5 24.9 - - + -
138C MET 3.2 12.8 - - - +
139C GLY* 3.9 0.4 - - - -
159C TYR* 3.4 24.2 - - - +
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Residues in contact with LEU 120 (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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81C ILE* 4.1 35.2 - - + -
82C LEU* 4.1 22.7 - - + -
86C SER* 6.2 0.4 - - - -
87C VAL 3.5 1.1 - - - +
88C LEU* 4.2 16.4 - - + -
119C PHE* 1.3 74.7 - - - +
121C GLY* 1.3 60.3 + - - +
122C PHE* 4.4 15.7 - - + -
136C VAL 3.8 0.9 - - - +
137C GLU* 3.3 2.3 - - - -
138C MET* 2.7 48.1 + - + +
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Residues in contact with GLY 121 (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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19A ILE* 3.8 27.4 - - - -
85C ASN 4.0 0.2 - - - +
86C SER* 3.0 5.7 - - - -
87C VAL* 2.8 43.7 + - - -
119C PHE* 4.0 3.3 - - - -
120C LEU* 1.3 74.6 - - - +
122C PHE* 1.3 64.4 + - - -
136C VAL 3.4 5.4 - - - -
137C GLU* 4.2 2.0 - - - -
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Residues in contact with PHE 122 (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 6.1 - - - +
82C LEU* 3.7 40.8 - - + -
85C ASN 3.3 6.7 - - - +
86C SER* 3.4 27.8 - - - -
120C LEU* 4.4 19.7 - - + -
121C GLY* 1.3 77.8 - - - -
123C ALA* 1.3 63.8 + - - +
124C THR* 3.6 5.3 + - - +
135C ASP* 3.6 3.8 - - - -
136C VAL* 2.7 55.2 + - + +
138C MET* 5.1 9.4 - - - -
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Residues in contact with ALA 123 (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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19A ILE* 3.8 9.4 - - + +
20A ALA* 4.5 15.3 - - + +
23A LEU* 3.5 28.9 - - + -
85C ASN* 2.8 30.9 + - - +
122C PHE* 1.3 70.6 - - - +
124C THR* 1.3 60.8 + - - +
134C ARG 3.5 7.9 - - - +
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Residues in contact with THR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C PHE* 4.1 7.6 - - - +
123C ALA* 1.3 76.2 - - - +
125C ASP* 1.3 73.5 + - - +
126C TYR* 3.2 18.2 + - - +
133C LEU* 3.2 29.1 + - + +
134C ARG* 2.9 36.8 + - - +
135C ASP 3.8 2.7 - - - +
136C VAL* 3.9 25.1 - - + -
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Residues in contact with ASP 125 (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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124C THR* 1.3 80.9 + - - +
126C TYR* 1.3 60.3 + - - +
127C ARG* 3.0 44.6 + - - +
132C THR* 4.1 7.6 - - - -
133C LEU 3.6 3.4 - - - -
134C ARG* 3.9 13.5 - - - +
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Residues in contact with TYR 126 (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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124C THR* 3.2 12.7 + - - +
125C ASP* 1.3 76.2 - - - +
127C ARG* 1.3 68.2 + - - +
128C PHE* 3.3 43.7 - + + +
131C TRP 3.8 0.7 - - - +
132C THR* 3.6 0.5 - - - -
133C LEU* 2.8 50.3 + - + -
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Residues in contact with ARG 127 (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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125C ASP* 3.0 45.8 + - - +
126C TYR* 1.3 85.0 - - - +
128C PHE* 1.3 63.8 + - - +
130C GLY* 5.9 2.9 - - - +
131C TRP 3.3 7.0 - - - +
132C THR* 3.7 23.4 + - + +
134C ARG* 5.1 8.3 - - - +
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Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR* 3.3 36.6 - + + +
127C ARG* 1.3 77.1 - - - +
129C ALA* 1.3 83.7 + - + +
130C GLY 3.3 1.5 - - - +
131C TRP* 2.8 28.1 + - + +
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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
------------------------------------------------------------
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