Contacts of the strand formed by residues 133 - 147 (chain A) in PDB entry 2ADS
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 ARG 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 5.8 4.2 - - - +
129A GLN 5.1 0.6 - - - -
130A GLY* 2.6 56.5 + - - +
131A LYS 3.8 12.9 + - - +
132A ASN* 1.3 82.8 - - + +
134A LYS* 1.3 60.9 + - - +
135A ILE* 4.3 29.3 - - + +
165A PRO* 5.6 3.1 - - + -
166A PHE 4.3 10.1 - - - +
167A GLU* 5.1 3.1 - - + +
259A LEU* 3.9 31.0 - - + -
261A TYR* 3.7 32.9 - - - -
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR* 3.3 29.0 + - + +
128A VAL 4.1 2.0 - - - -
129A GLN* 4.1 22.4 - - + +
130A GLY 4.5 2.5 - - - +
133A ARG* 1.3 72.5 - - - +
135A ILE* 1.3 65.8 + - - +
136A ALA* 5.9 0.9 - - + -
165A PRO* 3.4 5.0 - - - +
166A PHE* 3.3 55.6 + - + +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR* 3.7 5.4 - - - +
128A VAL* 2.7 45.8 + - + +
133A ARG* 4.3 32.3 - - + +
134A LYS* 1.3 82.5 - - - +
136A ALA* 1.3 62.0 + - - +
163A ILE* 3.0 37.5 - - + -
164A GLN 3.9 8.3 - - - +
165A PRO* 4.3 10.5 - - + -
166A PHE* 5.7 0.7 - - - -
259A LEU 4.3 15.7 - - - +
260A THR* 5.4 4.7 - - - +
261A TYR* 6.5 0.4 - - + -
269A ARG* 4.9 15.0 - - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 3.7 15.0 - - + +
127A THR* 4.0 19.3 - - + +
128A VAL* 4.5 0.9 - - - +
134A LYS* 5.9 1.1 - - - -
135A ILE* 1.3 76.5 - - - +
137A LEU* 1.4 62.6 - - - +
138A ILE* 3.4 11.9 + - + +
162A ARG 3.6 0.2 - - - +
163A ILE* 3.3 5.1 - - - -
164A GLN 3.0 34.9 + - - +
166A PHE* 5.1 11.6 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS 4.2 5.2 - - - +
126A ILE* 2.4 51.4 + - + +
128A VAL* 4.3 16.8 - - + -
136A ALA* 1.4 69.7 - - - +
138A ILE* 1.3 58.7 + - - +
139A PRO* 3.2 13.2 - - - +
161A PHE* 3.5 46.2 - - + -
162A ARG 3.9 1.1 - - - -
163A ILE* 3.8 26.4 - - + +
269A ARG* 5.7 0.7 - - - +
276A VAL* 6.1 6.5 - - + -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 3.4 26.9 - - + +
126A ILE* 5.2 1.3 - - + -
136A ALA* 4.0 15.3 - - + +
137A LEU* 1.3 70.5 - - - +
139A PRO* 1.3 67.4 - - + +
140A GLU* 3.5 1.0 + - - +
161A PHE* 3.4 0.6 - - - -
162A ARG* 2.8 43.1 + - + +
164A GLN* 3.7 15.7 - - + +
166A PHE* 5.7 8.1 - - + -
186A LYS* 3.9 15.0 - - - +
191A ASP* 3.6 26.9 - - + +
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Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 4.5 6.1 - - + +
118A PHE* 3.9 20.9 - - + -
119A TYR* 3.0 51.1 + - + -
126A ILE* 3.8 23.1 - - + -
137A LEU 3.2 8.0 - - - +
138A ILE* 1.3 83.0 - - + +
140A GLU* 1.3 58.0 + - - +
141A VAL* 4.1 11.9 - - + -
159A LEU* 6.1 0.2 - - + -
160A LYS 3.8 1.6 - - - +
161A PHE* 3.6 26.7 - - + -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 6.1 1.6 - - - -
138A ILE 3.9 1.6 - - - +
139A PRO* 1.3 72.2 - - - +
141A VAL* 1.3 60.3 + - - +
142A ASN* 3.7 13.2 - - - +
158A ASP* 3.2 8.8 - - - +
160A LYS* 2.7 47.7 + - - +
161A PHE 3.0 27.8 - - - +
162A ARG* 2.8 46.9 + - + +
8M G 5.1 4.9 - - - +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.2 11.6 - - - +
114A PHE* 4.8 23.8 - - + -
115A ILE* 4.8 15.9 - - + +
118A PHE* 6.2 4.9 - - + -
139A PRO* 4.1 11.2 + - + -
140A GLU* 1.3 77.3 - - - +
142A ASN* 1.3 65.2 + - - +
143A GLU* 3.9 8.3 - - - +
158A ASP 3.5 12.1 - - - +
159A LEU* 3.7 28.7 - - + +
290A ILE* 4.5 14.8 - - + -
294A TYR* 3.6 20.0 - - + +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 5.1 2.3 + - - +
140A GLU* 3.7 8.5 - - - +
141A VAL* 1.3 87.7 + - - +
143A GLU* 1.3 67.1 + - - +
157A LEU* 3.4 6.9 - - - +
158A ASP* 2.7 55.4 + - - +
294A TYR* 4.5 0.2 - - - -
8M G 2.7 44.1 + - - +
9M G 2.9 40.9 + - - +
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PHE* 4.0 29.6 - - + -
105A LEU* 5.7 0.4 - - - -
111A LYS* 2.6 48.7 + - - +
141A VAL 3.9 3.3 - - - +
142A ASN* 1.3 76.6 - - - +
144A LYS* 1.3 63.3 + - - +
155A LEU* 4.2 14.8 - - + -
156A HIS 3.9 5.4 - - - -
157A LEU* 4.5 1.8 - - - -
294A TYR* 3.1 42.8 + - + -
8M G 3.9 5.2 + - - +
9M G 3.3 22.5 + - - +
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PHE* 6.2 0.2 - - - -
143A GLU* 1.3 81.2 - - - +
145A VAL* 1.3 65.0 + - - +
146A LEU* 6.3 0.2 - - + -
155A LEU* 2.9 9.4 - - - +
156A HIS* 2.8 69.3 + - + +
157A LEU 4.3 3.1 - - - -
158A ASP* 3.7 26.7 + - + -
160A LYS* 5.5 7.4 - - - +
602A ASN* 4.0 15.2 + - - +
9M G 3.5 22.2 - - - +
10M G 2.8 42.2 + - - +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 5.5 5.6 - - + -
94A GLU* 4.4 19.4 - - + +
97A CYS* 4.0 38.4 - - + -
98A GLN* 5.8 3.1 - - + +
101A PHE* 5.0 17.9 - - + -
144A LYS* 1.3 80.1 - - - +
146A LEU* 1.3 87.3 + - - +
153A PHE* 5.3 6.7 - - + -
154A LEU 3.5 7.0 - - - +
155A LEU* 4.1 13.0 - - + -
156A HIS 5.4 0.4 - - - -
303A TRP* 6.4 0.4 - - + -
9M G 5.6 2.5 + - - -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.6 23.6 - - + -
94A GLU* 3.8 18.4 - - + +
144A LYS* 6.3 0.2 - - + -
145A VAL* 1.3 86.2 - - - +
147A LYS* 1.3 63.6 + - - +
153A PHE* 3.8 1.7 - - - +
154A LEU* 2.8 41.1 + - + +
156A HIS* 4.8 11.9 - - + -
604A PRO* 4.2 19.3 - - + -
620A LEU* 4.4 17.7 - - + -
626A ILE* 4.9 1.6 - - + -
642A LYS* 3.7 27.1 - - + +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE 2.8 19.9 + - - -
92A GLN* 2.6 34.3 + - - +
93A ASN* 5.1 0.9 - - - -
94A GLU* 3.3 22.0 + - + +
145A VAL* 6.0 0.2 - - + -
146A LEU* 1.3 78.0 - - - +
148A SER* 1.4 62.8 + - - +
151A GLY* 3.1 25.6 - - - +
152A TYR 3.2 18.4 - - - +
153A PHE* 3.8 16.2 - - + -
154A LEU* 3.7 5.4 - - - +
620A LEU* 3.6 6.3 - - - +
621A SER* 2.9 37.6 + - - +
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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