Contacts of the strand formed by residues 109 - 128 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TYR* 3.5 39.3 - + - +
146C GLY* 2.8 28.1 + - - +
270C HDS 3.6 29.8 - - + -
56D TYR* 5.4 0.3 - - - -
58D TRP* 3.9 9.4 + - - -
69D PHE* 3.9 15.5 - + - -
96D SER* 3.4 31.2 - - - -
97D TRP 3.6 9.4 - - - -
98D TRP* 3.6 23.3 - + + +
108D PRO* 1.3 74.4 - - - +
110D ARG* 1.3 62.0 + - - +
111D GLU 4.5 2.7 - - - +
112D THR* 3.6 20.2 - - - +
147D ARG* 3.5 17.1 + - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.6 36.6 - - - +
49D ASN* 5.2 3.2 + - - +
53D ILE* 4.2 17.0 - - + +
56D TYR* 3.9 14.4 + - - -
58D TRP* 3.7 25.4 - - + -
66D GLU* 2.8 45.5 + - - +
97D TRP* 2.9 38.6 + - - +
99D GLN* 4.1 3.6 - - + +
108D PRO 3.5 3.2 + - - -
109D PHE* 1.3 74.1 - - - +
111D GLU* 1.3 65.9 + - + +
147D ARG* 3.6 10.5 + - - -
247D GLU* 4.7 0.8 + - - -
248D SER* 4.4 3.0 + - - -
250D ILE* 3.8 11.9 - - - +
251D ASP* 3.0 32.7 + - - -
256D GLN* 5.6 0.4 - - - -
258D ARG* 3.6 8.9 - - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 5.4 1.0 + - - -
96D SER* 4.2 0.2 - - - -
97D TRP* 2.8 47.5 + - + +
109D PHE* 3.4 3.2 - - - -
110D ARG* 1.3 91.7 - - + +
112D THR* 1.3 68.1 + - - +
113D ASN* 2.6 29.3 + - - +
145D ASN* 3.3 26.8 + - - +
147D ARG* 4.3 10.0 + - - +
248D SER* 3.9 9.0 - - - -
249D LEU 3.5 1.2 + - - -
250D ILE* 3.1 44.4 + - + +
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TYR* 4.4 4.6 + - - +
94D GLN* 3.6 15.5 - - + +
95D LYS 3.2 7.2 - - - +
96D SER* 3.2 25.2 + - - +
109D PHE* 3.6 15.1 - - - +
111D GLU* 1.3 77.7 + - - +
113D ASN* 1.3 73.7 + - - +
114D TYR* 3.4 40.4 + - + +
145D ASN* 3.2 25.0 + - - +
147D ARG* 4.9 5.2 + - - +
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Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR 3.8 0.9 - - - +
94D GLN* 3.3 8.0 - - - +
95D LYS* 2.7 47.6 + - + +
97D TRP* 4.0 10.7 - - + -
111D GLU* 2.6 29.5 + - - -
112D THR* 1.3 81.1 + - - +
114D TYR* 1.3 62.5 + - - +
115D GLU* 4.1 1.3 - - + +
143D ASP* 3.9 13.0 - - - +
144D SER 3.4 2.0 - - - -
145D ASN* 3.6 7.9 - - - +
247D GLU 4.6 0.3 - - - +
248D SER* 3.3 11.1 - - - -
249D LEU* 3.0 33.0 + - - +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PHE* 5.0 0.7 - + - -
94C GLN* 5.1 2.2 - - - -
96C SER* 5.1 0.4 - - - -
109C PHE* 3.4 45.3 - + - +
112C THR* 4.3 6.2 + - + +
114C TYR* 5.0 3.5 + - - -
92D TYR* 3.1 28.0 - + + +
93D THR 3.9 2.2 - - - -
94D GLN* 4.1 6.1 - - - -
112D THR* 3.4 36.1 + - + +
113D ASN* 1.3 73.0 - - - +
115D GLU* 1.3 58.8 + - - +
116D PRO* 3.3 9.1 - - - +
142D HIS 3.5 0.3 - - - +
143D ASP* 3.6 0.8 - - - -
144D SER 2.8 39.8 + - - -
145D ASN 3.5 26.2 - - - -
146D GLY* 3.8 8.9 - - - -
270D HDS 3.8 26.3 + - + -
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D SER* 4.4 0.5 + - - -
92D TYR* 3.6 5.4 - - - -
93D THR* 2.7 47.7 + - - +
95D LYS* 4.3 22.3 + - - -
113D ASN* 5.3 1.6 - - + +
114D TYR* 1.3 73.2 - - - +
116D PRO* 1.3 63.0 - - - +
117D GLN* 3.9 6.2 + - + +
141D ASN* 2.8 32.4 + - - +
142D HIS 3.3 8.5 - - - +
143D ASP* 4.0 17.5 - - - +
157D ARG* 3.7 12.8 + - - -
174D LYS* 4.3 9.0 + - - -
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Residues in contact with PRO 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TRP* 6.2 0.4 - - + -
91D SER 3.4 9.2 - - - +
92D TYR* 4.3 3.8 - - + -
114D TYR 3.3 10.5 - - - +
115D GLU* 1.3 85.3 - - - +
117D GLN* 1.3 62.6 + - - +
140D TYR* 4.2 1.6 - - + +
141D ASN* 3.7 0.3 - - - -
142D HIS* 3.1 52.9 + - + +
270D HDS 4.1 39.0 - - + -
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 2.9 33.6 + - - -
90D ALA* 3.2 9.3 - - - +
91D SER* 2.9 50.3 + - - +
115D GLU* 4.4 6.1 - - - +
116D PRO* 1.3 76.3 - - - +
118D LEU* 1.3 61.4 + - - +
119D PHE* 4.2 2.6 - - + -
137D GLU* 3.9 0.4 + - - -
140D TYR* 3.3 7.4 - - - +
141D ASN* 2.8 30.3 + - + +
159D TYR* 3.2 24.9 + - - +
174D LYS* 2.8 26.2 + - - -
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 4.1 14.1 - - + -
88D LEU* 3.9 20.2 - - + -
89D GLY 3.4 16.4 - - - +
90D ALA* 4.6 4.3 - - + -
117D GLN* 1.3 75.1 - - - +
119D PHE* 1.3 63.0 + - - +
139D GLY* 3.1 1.9 - - - -
140D TYR* 2.8 46.2 + - + +
159D TYR* 4.5 0.2 + - - -
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.1 8.5 - - + -
22B MET* 3.4 36.3 - - + -
35D TYR* 4.0 9.2 - + - -
87D VAL* 4.9 1.8 - - + -
88D LEU* 3.4 9.3 - - - +
89D GLY* 2.9 49.9 + - - +
90D ALA 3.8 23.3 - - - -
91D SER* 3.8 13.0 - - - -
117D GLN* 4.2 7.6 - - + -
118D LEU* 1.3 79.0 - - - +
120D LEU* 1.3 61.8 + - - +
121D GLY 4.1 7.4 - - - -
137D GLU* 3.5 24.7 - - + -
138D MET 3.2 13.2 - - - +
139D GLY* 3.9 0.2 - - - -
159D TYR* 3.4 24.0 - - - +
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Residues in contact with LEU 120 (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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81D ILE* 3.6 34.1 - - + -
82D LEU* 3.3 29.4 - - + -
86D SER* 5.8 0.2 - - - -
87D VAL 3.4 5.8 - - - +
88D LEU* 4.2 12.8 - - + -
119D PHE* 1.3 74.0 - - - +
121D GLY* 1.3 59.4 + - - +
122D PHE* 4.0 20.8 - - + -
136D VAL 4.0 0.9 - - - +
137D GLU* 3.4 1.6 - - - -
138D MET* 2.8 40.3 + - + +
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Residues in contact with GLY 121 (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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19B ILE* 3.8 26.7 - - - -
86D SER* 3.1 6.6 - - - -
87D VAL* 2.7 39.9 + - - +
119D PHE* 4.0 4.2 - - - -
120D LEU* 1.3 74.0 - - - +
122D PHE* 1.3 64.7 + - - -
136D VAL 3.4 6.1 - - - -
137D GLU* 4.2 2.2 - - - -
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Residues in contact with PHE 122 (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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19B ILE* 3.8 7.4 - - - +
82D LEU* 3.4 38.8 - - + -
85D ASN* 3.4 19.1 - - - +
86D SER* 3.4 26.9 - - - -
120D LEU* 4.0 24.5 - - + -
121D GLY* 1.3 75.3 - - - -
123D ALA* 1.3 61.0 + - - +
124D THR* 3.7 15.6 + - + +
135D ASP* 3.6 4.3 - - - -
136D VAL* 2.7 53.6 + - + +
137D GLU* 5.8 0.2 - - - -
138D MET* 6.5 0.9 - - + -
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Residues in contact with ALA 123 (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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19B ILE* 3.7 9.0 - - + +
20B ALA* 4.5 15.3 - - + -
23B LEU* 3.7 27.8 - - + -
85D ASN* 2.8 38.3 + - + +
122D PHE* 1.3 70.5 - - - +
124D THR* 1.3 60.6 + - - +
134D ARG 3.4 8.1 - - - +
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Residues in contact with THR 124 (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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85D ASN* 4.8 4.7 - - - +
122D PHE* 4.0 21.5 - - + +
123D ALA* 1.3 79.4 - - - +
125D ASP* 1.3 62.6 + - - +
126D TYR* 4.3 7.9 - - - -
133D LEU* 2.8 43.1 + - + +
134D ARG* 2.9 33.7 + - - +
135D ASP 3.9 0.3 + - - -
136D VAL* 4.2 14.2 - - + +
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Residues in contact with ASP 125 (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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124D THR* 1.3 72.7 - - - +
126D TYR* 1.3 67.3 + - - +
127D ARG* 2.8 51.4 + - - +
132D THR* 3.8 4.0 - - - +
133D LEU 3.7 2.5 - - - -
134D ARG* 3.1 24.7 + - - -
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Residues in contact with TYR 126 (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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124D THR* 4.3 4.2 - - - +
125D ASP* 1.3 73.3 - - - +
127D ARG* 1.3 63.2 + - - +
128D PHE* 4.5 29.1 - + + +
131D TRP 3.6 1.2 - - - +
132D THR* 3.3 2.6 - - - -
133D LEU* 2.7 63.7 + - + +
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ASP* 2.8 42.7 + - - +
126D TYR* 1.3 74.6 - - - +
128D PHE* 1.3 68.9 + - - +
130D GLY* 5.5 5.8 - - - +
131D TRP 3.6 2.9 - - - +
132D THR* 3.6 28.4 + - - +
134D ARG* 4.3 6.3 - - - +
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 4.5 25.6 - + + +
127D ARG* 1.3 77.8 - - - +
129D ALA* 1.3 79.3 + - + +
130D GLY 3.3 0.8 - - - +
131D TRP* 2.9 37.7 + - + +
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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