Contacts of the strand formed by residues 142 - 161 (chain A) in PDB entry 1PNG
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 TYR 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 3.8 27.5 - - + +
104A LYS* 4.8 0.9 - - - +
140A TYR* 3.3 3.7 - - - +
141A LYS* 1.3 94.5 - - + +
143A SER* 1.3 61.5 + - - +
302A LYS* 3.3 5.9 - - - +
303A SER 2.9 32.1 + - - +
304A ASN 3.8 13.5 - - - -
305A THR 3.5 27.1 - - - +
306A PRO* 3.7 39.4 - - + +
307A ILE* 4.1 11.7 - - + +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR 4.8 1.2 + - - -
102A ASP* 4.3 10.5 + - - -
104A LYS* 3.9 30.0 - - - +
105A SER* 3.7 19.3 + - - -
140A TYR 6.0 0.2 - - - -
142A TYR* 1.3 79.0 - - - +
144A ALA* 1.3 62.7 + - - +
300A ILE* 4.5 6.3 - - - -
301A ALA 3.1 7.0 - - - -
302A LYS* 3.7 27.4 - - - -
307A ILE* 4.2 5.7 - - - +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 4.6 5.6 - - - -
143A SER* 1.3 75.8 - - - +
145A VAL* 1.3 61.3 - - - +
299A VAL 3.8 0.8 - - - +
300A ILE* 3.3 6.0 - - - +
301A ALA* 2.8 34.4 + - + +
307A ILE* 4.3 10.3 - - + +
308A SER 3.8 11.0 - - - +
309A ALA* 3.7 30.3 - - + +
310A PRO* 4.0 6.0 - - + +
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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
----------------------------------------------------------
69A ASN* 5.4 1.6 + - - -
76A TYR* 3.8 12.4 + - + -
102A ASP 3.6 22.9 - - - +
103A PHE* 3.9 18.2 - - + -
105A SER* 4.1 4.6 + - - +
106A LEU* 3.6 29.6 - - + +
144A ALA* 1.3 76.7 - - - +
146A VAL* 1.3 72.2 + - - +
298A PHE* 3.9 26.0 - - + -
299A VAL 3.3 11.7 - - - +
300A ILE* 3.9 15.7 - - + -
309A ALA* 4.9 2.3 - - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 4.3 7.2 - - - +
145A VAL* 1.3 81.7 - - - +
147A PRO* 1.3 86.4 - - + +
298A PHE* 3.4 5.2 - - - -
299A VAL* 2.9 40.2 + - + +
309A ALA* 3.5 28.9 - - + -
310A PRO* 3.7 16.4 - - + +
312A VAL* 3.7 20.0 - - + +
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Residues in contact with PRO 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.6 24.0 - - - +
76A TYR* 3.4 31.0 - - + +
146A VAL* 1.3 103.4 - - + +
148A VAL* 1.3 63.5 + - - +
149A ILE 4.5 2.2 - - - +
150A GLN* 4.1 20.4 - - + +
297A SER 3.6 2.0 - - - +
298A PHE* 3.5 24.0 - - + -
312A VAL* 3.6 9.6 - - - +
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Residues in contact with VAL 148 (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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147A PRO* 1.3 76.7 - - - +
149A ILE* 1.3 66.1 + - + +
171A LYS* 3.7 34.2 - - + +
173A ILE* 3.8 24.9 - - + -
184A LEU* 4.4 7.4 - - + -
275A TYR* 3.6 42.4 - - + -
297A SER* 2.8 18.7 + - - +
298A PHE 4.3 1.6 - - - -
299A VAL* 4.1 21.5 - - + +
312A VAL* 4.2 8.5 - - + +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PRO* 4.9 1.1 - - - -
148A VAL* 1.3 86.7 - - + +
150A GLN* 1.3 68.4 + - - +
151A TYR* 3.9 11.0 - - + +
168A GLY 3.7 23.6 - - - +
169A LEU* 3.6 26.2 - - + -
171A LYS* 4.0 16.4 - - + -
275A TYR* 3.7 22.9 - - + +
277A TYR* 4.4 2.9 - - + -
295A ILE* 4.0 25.1 - - + -
296A SER* 3.5 0.8 - - - -
297A SER* 3.1 39.0 + - - +
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Residues in contact with GLN 150 (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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66A TYR* 4.3 2.4 - - - -
74A GLU* 4.1 12.5 + - - +
75A TRP 3.0 23.3 + - - +
76A TYR* 4.0 3.8 - - - +
77A GLU* 3.1 21.1 + - - +
147A PRO* 4.1 21.1 - - + +
149A ILE* 1.3 84.9 - - - +
151A TYR* 1.3 69.8 + - - +
152A ASN* 3.1 32.0 + - - +
295A ILE 3.7 3.8 - - - -
296A SER* 4.1 6.3 - - - -
298A PHE* 3.8 10.7 - - + -
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.9 15.9 - - + +
150A GLN* 1.3 80.8 - - - +
152A ASN* 1.3 55.0 + - - +
153A LYS 4.0 0.4 - - - -
157A ASP 4.2 13.2 - - - +
158A GLY* 3.6 3.5 - - - -
159A VAL* 3.7 35.7 - - + +
167A LEU 5.5 1.3 - - - -
168A GLY* 2.9 38.4 + - - -
169A LEU* 3.7 14.6 - - + -
171A LYS* 5.4 3.3 + - - -
294A ALA* 3.3 7.4 - - - -
295A ILE* 2.8 36.0 + - + +
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Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 2.7 29.8 + - - +
64A ASN* 3.1 12.8 + - - -
66A TYR* 3.4 12.8 + - - -
77A GLU* 3.0 35.5 + - - +
80A ARG* 3.9 8.3 - - - +
150A GLN* 3.1 35.0 + - - +
151A TYR* 1.3 79.7 - - - +
153A LYS* 1.3 67.6 + - - +
154A SER 3.2 4.7 - - - +
294A ALA* 4.4 3.6 - - - -
295A ILE 3.9 2.0 - - - +
296A SER* 3.4 8.7 - - - -
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Residues in contact with LYS 153 (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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62A TYR* 4.2 0.2 - - - -
64A ASN* 4.8 0.2 + - - -
66A TYR* 3.9 11.2 + - - +
116A TYR* 3.4 25.3 - - + -
151A TYR 4.0 0.2 - - - -
152A ASN* 1.3 79.9 + - - +
154A SER* 1.3 61.8 + - - +
157A ASP* 4.0 26.9 + - + +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 3.6 17.3 - - - -
116A TYR* 3.5 19.5 - - - -
118A GLU* 3.6 10.5 + - - -
152A ASN 3.2 2.0 - - - -
153A LYS* 1.3 80.4 - - - +
155A SER* 1.3 65.6 + - - +
156A ILE* 3.5 10.2 + - - +
157A ASP* 2.7 40.1 + - - +
158A GLY 3.6 6.6 + - - -
294A ALA* 4.1 8.7 - - - +
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Residues in contact with SER 155 (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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62A TYR* 3.8 27.1 - - - -
118A GLU* 2.6 32.0 + - - -
154A SER* 1.3 73.0 - - - +
156A ILE* 1.3 62.8 + - - +
157A ASP 3.5 0.3 + - - -
158A GLY* 3.8 2.6 + - - -
191A TRP* 3.7 36.6 + - - +
292A PHE* 3.3 23.9 - - - +
294A ALA* 4.7 5.9 + - - +
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Residues in contact with ILE 156 (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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118A GLU* 3.7 12.3 - - - +
120A TRP* 5.3 9.0 - - + -
154A SER* 3.2 11.4 - - - +
155A SER* 1.3 85.9 + - - +
157A ASP* 1.3 62.5 + - - +
158A GLY 3.4 3.8 - - - -
191A TRP* 3.9 37.5 - - + +
292A PHE* 3.6 32.8 - - + -
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Residues in contact with ASP 157 (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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151A TYR* 4.2 16.7 - - - +
152A ASN 4.5 0.3 + - - -
153A LYS* 4.0 25.8 + - + +
154A SER* 2.7 39.6 + - - +
156A ILE* 1.3 83.7 - - - +
158A GLY* 1.3 66.0 + - - +
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Residues in contact with GLY 158 (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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151A TYR* 3.6 15.7 - - - -
154A SER 3.6 4.2 + - - -
155A SER 3.8 2.6 + - - -
156A ILE 3.4 3.6 - - - -
157A ASP* 1.3 84.1 - - - +
159A VAL* 1.3 65.6 + - - -
160A PRO* 3.6 6.9 - - - +
292A PHE* 3.8 10.4 - - - +
293A TYR 3.0 18.2 - - - -
294A ALA* 3.9 3.8 - - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 3.7 36.8 - - + -
158A GLY* 1.3 71.6 - - - -
160A PRO* 1.3 79.2 - - + +
161A TYR* 3.4 0.9 + - - +
166A THR* 3.8 24.0 - - + -
167A LEU 5.3 2.9 - - - +
169A LEU* 4.2 14.1 - - + -
279A PHE* 3.8 21.5 - - + -
292A PHE* 3.3 1.8 - - - -
293A TYR* 2.6 37.5 + - - +
295A ILE* 3.9 12.1 - - + -
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Residues in contact with PRO 160 (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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158A GLY 3.6 4.7 - - - +
159A VAL* 1.3 98.9 - - + +
161A TYR* 1.3 59.9 + - - +
162A GLY 4.1 0.5 + - - -
163A LYS* 3.9 26.8 - - + +
166A THR* 4.2 18.4 + - + +
279A PHE* 4.9 3.8 - - - -
291A ALA 3.6 7.9 - - - +
292A PHE* 3.8 18.8 - - + -
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL 3.4 1.5 + - - +
160A PRO* 1.3 74.5 - - - +
162A GLY* 1.3 69.8 + - - +
163A LYS* 4.7 3.9 - - - +
204A CYS* 4.1 14.1 - - + -
205A ALA* 4.1 10.8 - - + -
210A ARG* 3.1 24.3 + - + +
212A HIS* 4.6 0.7 - + - -
279A PHE* 3.8 24.2 - + + -
280A GLN* 2.6 29.8 + - - +
281A SER* 5.3 0.2 - - - -
282A TRP* 3.3 51.8 - + + +
284A ASN* 4.1 5.5 - - - +
291A ALA* 3.0 27.4 + - + +
292A PHE 4.6 0.7 - - - +
293A TYR* 3.5 45.8 - + + -
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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