Contacts of the strand formed by residues 291 - 303 (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 ALA 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A PRO* 3.6 3.3 - - - +
161A TYR* 3.0 46.4 + - + +
163A LYS* 5.9 2.4 - - - +
191A TRP 3.3 7.0 - - - -
194A ALA* 4.2 2.2 - - + -
204A CYS 3.4 20.2 - - - +
205A ALA* 3.7 7.4 - - + +
282A TRP* 4.2 11.0 - - + -
284A ASN* 4.4 2.6 + - - +
290A ASP* 1.3 76.3 - - - +
292A PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 292 (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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155A SER 3.3 18.8 - - - +
156A ILE* 3.6 38.6 - - + -
158A GLY 3.8 20.9 - - - +
159A VAL 3.3 6.5 - - - +
160A PRO* 3.8 23.3 - - + -
161A TYR* 4.4 0.7 - - - +
190A GLY* 3.2 3.8 - - - -
191A TRP* 3.0 52.4 + + + +
205A ALA* 3.7 4.5 - - - +
290A ASP* 3.5 36.1 - - + -
291A ALA* 1.3 77.7 - - - +
293A TYR* 1.3 62.8 + - - +
294A ALA 4.1 0.4 - - - -
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Residues in contact with TYR 293 (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* 3.0 2.0 - - - -
159A VAL* 2.6 40.1 + - - +
161A TYR* 3.5 40.7 - + + -
188A ILE* 4.0 15.5 - - + -
189A SER 3.5 3.6 - - - -
190A GLY* 3.6 17.0 - - - -
205A ALA* 3.7 22.8 + - + +
208A CYS* 4.6 3.1 + - - -
210A ARG* 3.5 18.9 - - - +
212A HIS* 3.1 33.4 + + - -
226A LEU* 3.7 21.6 - - + +
279A PHE* 3.5 37.7 - + + -
292A PHE* 1.3 72.2 - - - +
294A ALA* 1.3 60.9 + - - +
295A ILE* 3.6 2.6 + - + +
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Residues in contact with ALA 294 (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* 3.6 29.2 - - + +
80A ARG* 2.8 32.9 + - - +
151A TYR 3.3 8.7 - - - +
152A ASN* 4.4 0.2 - - - -
154A SER 4.1 11.4 - - - +
155A SER* 4.7 5.5 + - - +
158A GLY* 3.9 4.2 - - - -
188A ILE* 3.3 2.6 - - - +
189A SER* 2.9 22.7 + - - +
292A PHE 4.1 1.2 - - - -
293A TYR* 1.3 71.0 - - - +
295A ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 295 (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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80A ARG* 3.4 3.6 - - - +
149A ILE* 4.0 15.7 - - + -
150A GLN* 3.7 1.4 + - - -
151A TYR* 2.8 53.3 + - + +
152A ASN* 3.9 0.2 - - - +
159A VAL* 3.9 27.4 - - + -
169A LEU* 4.8 1.8 - - + -
186A THR* 4.0 7.2 - - + -
187A THR 3.4 10.1 - - - +
188A ILE* 4.2 13.2 - - + -
277A TYR* 3.8 49.4 - - + -
279A PHE* 5.0 4.9 - - + -
293A TYR 4.2 2.5 - - - +
294A ALA* 1.3 75.5 - - - +
296A SER* 1.3 70.8 + - - +
297A SER* 5.1 0.2 - - - -
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Residues in contact with SER 296 (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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77A GLU* 2.8 28.6 + - - +
149A ILE 3.5 6.1 - - - -
150A GLN* 4.1 3.8 - - - -
152A ASN* 3.4 14.1 - - - -
185A ARG 3.8 1.2 + - - +
186A THR* 3.2 5.0 - - - +
187A THR* 2.9 43.8 + - - -
295A ILE* 1.3 74.9 - - - +
297A SER* 1.3 61.3 + - - +
298A PHE* 3.8 22.0 - - - -
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Residues in contact with SER 297 (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* 3.6 2.6 - - - +
148A VAL* 2.8 31.5 + - - -
149A ILE* 3.1 23.5 + - - +
184A LEU* 4.7 4.5 - - - +
185A ARG 3.2 5.5 + - - -
186A THR* 2.9 23.4 + - - -
275A TYR* 2.9 36.7 + - - -
296A SER* 1.3 75.7 - - - +
298A PHE* 1.3 59.6 + - - +
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Residues in contact with PHE 298 (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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76A TYR* 3.8 23.6 - + + -
77A GLU 3.3 40.6 - - - -
103A PHE* 4.0 12.3 - + - -
145A VAL* 3.9 22.0 - - + -
146A VAL 3.4 7.4 - - - +
147A PRO* 3.5 31.4 - - + -
148A VAL* 4.3 4.0 - - - +
150A GLN* 3.8 12.3 - - + -
183A TYR 3.8 0.2 - - - +
184A LEU* 3.1 7.8 - - - +
185A ARG* 2.7 53.4 + - + +
296A SER* 3.8 21.8 - - - -
297A SER* 1.3 76.6 - - - +
299A VAL* 1.3 59.8 + - - +
300A ILE* 4.0 7.2 - - + -
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Residues in contact with VAL 299 (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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144A ALA 3.8 0.3 - - - +
145A VAL* 3.3 4.7 - - - +
146A VAL* 2.9 40.5 + - + +
148A VAL* 4.1 11.1 - - + +
173A ILE* 4.3 16.2 - - + -
175A LEU* 4.0 25.8 - - + -
183A TYR 3.5 8.1 - - - +
184A LEU* 4.1 16.2 - - + -
264A LEU* 4.3 11.0 - - + -
298A PHE* 1.3 73.0 - - - +
300A ILE* 1.3 66.2 + - - +
301A ALA 4.2 0.4 + - - -
310A PRO* 3.9 24.1 - - + +
312A VAL* 4.5 3.8 - - + -
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Residues in contact with ILE 300 (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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102A ASP* 3.9 24.5 - - + +
143A SER* 4.5 6.1 - - - -
144A ALA 3.3 8.5 - - - +
145A VAL* 3.9 23.6 - - + -
181A LYS 3.9 0.3 - - - +
182A ALA* 3.2 7.1 - - - +
183A TYR* 2.9 65.3 + - + +
185A ARG* 3.7 30.1 - - + -
298A PHE* 3.9 4.0 - - + +
299A VAL* 1.3 81.1 - - - +
301A ALA* 1.3 63.7 + - - +
302A LYS* 4.0 21.3 - - + -
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Residues in contact with ALA 301 (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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143A SER* 3.1 4.5 - - - -
144A ALA* 2.8 36.6 + - + +
175A LEU* 4.5 3.4 - - + -
176A PRO* 4.3 1.8 - - + -
179A THR* 3.9 13.9 - - + +
181A LYS 3.7 3.6 - - - -
182A ALA* 4.6 0.2 - - - +
299A VAL 4.2 0.6 + - - -
300A ILE* 1.3 73.9 - - - +
302A LYS* 1.3 60.7 + - - +
307A ILE* 3.7 26.6 - - + +
310A PRO* 3.8 25.8 - - + -
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Residues in contact with LYS 302 (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 THR* 5.6 9.3 - - - +
102A ASP* 4.5 4.4 + - - +
104A LYS* 6.4 0.9 - - - +
140A TYR* 3.9 32.2 - - + -
142A TYR 3.3 5.6 - - - +
143A SER* 3.7 20.0 - - - -
179A THR* 3.7 1.4 - - - +
180A GLU* 2.8 25.5 + - - -
181A LYS* 2.7 29.2 + - + +
183A TYR* 2.9 39.6 + - + -
300A ILE* 4.0 10.1 - - + -
301A ALA* 1.3 78.8 - - - +
303A SER* 1.3 61.7 + - - +
307A ILE* 4.6 1.6 - - - -
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Residues in contact with SER 303 (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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140A TYR* 3.8 12.4 - - - +
141A LYS 3.5 2.8 + - - -
142A TYR* 2.9 33.4 + - - +
178A ASN* 2.8 29.3 + - - -
180A GLU* 2.8 18.3 + - - -
302A LYS* 1.3 78.5 - - - +
304A ASN* 1.3 57.8 + - - +
305A THR* 2.9 31.8 + - - -
307A ILE* 4.2 9.0 - - - -
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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