Contacts of the strand formed by residues 169 - 186 (chain A) in PDB entry 3C0M
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A VAL* 4.2 17.9 - - + -
151A ILE 3.7 3.6 - - - -
152A ARG* 4.4 17.3 - - - +
167A LYS 3.6 1.9 + - - +
168A THR* 1.3 76.0 - - - +
170A ILE* 1.3 69.9 + - - +
171A LYS* 3.9 3.4 - - + +
317A THR 3.7 0.3 - - - +
318A LEU* 3.6 0.7 - - - -
319A SER* 2.9 47.6 + - - +
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Residues in contact with ILE 170 (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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112A PHE* 5.0 0.4 - - + -
116A THR* 4.0 24.7 - - - +
117A SER* 4.8 11.9 - - - +
120A ALA* 4.0 20.2 - - + -
128A VAL* 4.9 5.8 - - + -
140A MET* 5.1 1.3 - - + -
149A TRP 3.7 2.4 - - - +
150A VAL* 4.6 0.9 - - - -
151A ILE* 2.8 54.7 + - + +
168A THR* 4.2 8.3 - - + +
169A ALA* 1.3 83.6 - - - +
171A LYS* 1.3 58.9 - - - +
172A VAL* 3.7 6.3 + - + +
316A LEU* 4.3 16.8 - - + -
317A THR 3.5 2.0 - - - -
318A LEU* 3.4 29.4 - - + -
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Residues in contact with LYS 171 (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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145A ASP* 4.6 19.0 + - - -
148A GLY* 3.6 17.0 - - - +
149A TRP 3.3 9.2 - - - +
150A VAL* 4.2 13.2 - - + +
169A ALA* 3.9 3.0 - - + -
170A ILE* 1.3 73.9 - - - +
172A VAL* 1.3 61.6 + - - +
173A SER* 3.2 32.9 + - - +
315A ASP 3.6 2.6 - - - +
316A LEU* 3.6 2.3 - - - +
317A THR* 2.8 59.3 + - + +
319A SER* 5.9 1.8 - - - +
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Residues in contact with VAL 172 (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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105A LEU* 5.5 0.2 - - + -
106A VAL* 5.0 6.5 - - + -
112A PHE* 3.3 36.6 - - + -
148A GLY* 3.0 2.1 - - - -
149A TRP* 2.7 47.9 + - + +
151A ILE* 4.8 4.9 - - + -
170A ILE* 4.4 8.3 - - + +
171A LYS* 1.3 75.8 - - - +
173A SER* 1.3 62.0 + - - +
175A PHE* 3.2 35.1 - - + -
314A TYR* 4.1 17.7 - - + -
315A ASP 3.5 3.4 - - - -
316A LEU* 4.0 8.1 - - + -
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Residues in contact with SER 173 (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 ASP* 5.7 0.9 - - - -
148A GLY* 3.7 11.7 - - - -
171A LYS* 3.2 31.8 + - - +
172A VAL* 1.3 75.8 - - - +
174A ASN* 1.3 74.1 + - - +
175A PHE* 3.4 10.0 + - - -
314A TYR* 3.5 4.3 - - - +
315A ASP* 2.9 33.6 + - - +
317A THR* 5.2 3.1 + - - -
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Residues in contact with ASN 174 (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 ASP* 5.7 4.6 - - - +
148A GLY 5.5 0.6 - - - +
173A SER* 1.3 82.8 - - - +
175A PHE* 1.3 64.5 + - - +
176A ALA* 3.9 3.3 + - - +
313A SER 4.6 0.3 - - - -
314A TYR* 3.6 11.1 - - - -
315A ASP* 3.0 36.0 + - + +
349A LYS* 5.9 4.6 - - - +
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Residues in contact with PHE 175 (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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98A GLU* 4.7 1.3 - - - +
102A GLN* 3.7 40.8 - - + +
105A LEU* 4.2 15.5 - - + -
106A VAL* 4.7 3.6 - - + -
147A ASP 5.0 4.9 - - - -
149A TRP* 4.1 12.8 - + - -
172A VAL* 3.2 35.0 - - + -
173A SER* 4.3 7.0 - - - -
174A ASN* 1.3 80.2 - - - +
176A ALA* 1.3 59.0 + - - +
177A TYR* 3.5 26.8 - + + +
312A VAL* 4.2 12.1 - - + -
313A SER 3.5 6.7 - - - -
314A TYR* 3.7 29.8 - + + -
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Residues in contact with ALA 176 (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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174A ASN* 4.9 3.8 - - - +
175A PHE* 1.3 76.0 - - - +
177A TYR* 1.3 75.0 + - - +
178A ASN* 4.1 2.2 - - + +
313A SER* 3.1 44.9 + - - +
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Residues in contact with TYR 177 (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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98A GLU* 2.4 42.8 + - - +
101A VAL* 4.9 10.3 - - + -
102A GLN* 3.3 13.1 + - + +
175A PHE* 3.5 20.3 - + + +
176A ALA* 1.3 88.9 - - - +
178A ASN* 1.3 62.2 + - - +
235A LEU* 3.6 33.9 - - + -
238A LYS* 3.5 28.0 + - + +
239A VAL* 3.3 30.3 - - + +
240A THR* 3.4 6.3 + - - -
310A ALA* 4.4 13.9 - - + -
311A ASP 3.3 6.5 - - - +
312A VAL* 3.9 29.2 - - + -
398A ALA* 5.6 0.4 - - + -
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Residues in contact with ASN 178 (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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176A ALA* 4.1 2.2 - - + -
177A TYR* 1.3 72.4 - - - +
179A LEU* 1.3 72.1 + - - +
180A ASP* 3.5 1.4 + - - -
240A THR* 3.4 16.2 + - - +
241A THR 4.2 0.8 - - - -
242A LYS* 3.1 46.4 + - - +
310A ALA* 4.0 0.7 - - - -
311A ASP* 2.8 47.9 + - + +
313A SER* 5.8 0.4 + - - -
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Residues in contact with LEU 179 (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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177A TYR 3.7 2.6 + - - -
178A ASN* 1.3 80.8 - - - +
180A ASP* 1.3 60.3 + - - +
181A PRO* 3.1 15.9 - - - +
239A VAL* 4.2 16.6 - - + -
240A THR 3.0 16.9 + - - +
241A THR* 3.5 12.8 - - + +
245A PHE* 3.7 24.9 - - + -
265A TRP* 3.9 35.7 - - + -
308A PHE* 3.7 44.0 - - + -
309A LYS 3.7 6.3 - - - +
310A ALA* 4.0 4.2 - - + +
400A ILE* 4.6 12.8 - - + -
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Residues in contact with ASP 180 (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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178A ASN 3.5 1.2 + - - -
179A LEU* 1.3 71.4 - - - +
181A PRO* 1.3 63.5 - - - +
182A ASP* 3.0 25.1 + - - +
183A SER* 2.5 46.4 + - - +
308A PHE* 4.1 4.5 - - - -
309A LYS* 2.7 19.3 + - + +
311A ASP* 3.8 21.3 - - - +
397A ARG* 4.8 8.1 + - - -
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Residues in contact with PRO 181 (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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179A LEU* 3.1 14.5 - - + +
180A ASP* 1.3 85.6 - - - +
182A ASP* 1.3 70.2 + - - +
183A SER 3.2 1.2 + - - -
184A PHE* 3.6 17.5 + - - +
241A THR* 4.3 9.0 - - + -
243A ASN* 5.8 5.6 - - - +
245A PHE* 3.5 38.9 - - + -
248A PRO* 6.0 0.3 - - - +
308A PHE* 4.0 14.5 - - + -
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Residues in contact with ASP 182 (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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180A ASP* 2.9 17.0 + - - +
181A PRO* 1.3 84.2 - - - +
183A SER* 1.3 58.0 + - - +
184A PHE* 3.2 7.9 + - - +
185B LYS* 4.8 6.8 + - - -
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Residues in contact with SER 183 (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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180A ASP* 2.5 30.8 + - - +
182A ASP* 1.3 77.4 - - - +
184A PHE* 1.3 67.3 + - - +
185A LYS* 3.4 6.6 + - - +
307A GLU 3.4 7.8 - - - +
308A PHE* 4.1 2.1 - - - -
309A LYS* 2.8 46.9 + - - +
397A ARG* 4.8 6.1 - - - -
185B LYS* 4.2 10.7 - - - +
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Residues in contact with PHE 184 (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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180A ASP 4.3 0.6 + - - -
181A PRO 3.6 15.8 + - - +
182A ASP 3.2 4.5 + - - +
183A SER* 1.3 80.9 + - - +
185A LYS* 1.3 73.6 + - - +
186A HIS* 3.6 40.6 - + + -
247A TRP* 4.4 2.0 - - - -
248A PRO* 3.4 41.5 - - + -
249A LEU 5.2 0.7 - - - -
250A VAL* 4.1 4.7 - - + -
304A TYR* 3.7 18.2 - + - -
306A TYR* 4.1 13.9 - - + -
307A GLU 3.6 4.7 - - - -
308A PHE* 3.6 28.5 - + + -
185B LYS* 3.6 12.8 + - - -
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Residues in contact with LYS 185 (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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183A SER 4.0 4.3 - - - +
184A PHE* 1.3 86.9 - - - +
186A HIS* 1.3 73.3 + - - +
306A TYR* 3.3 3.3 - - - -
307A GLU* 2.8 60.2 + - + +
185B LYS* 4.4 24.0 - - + -
186B HIS 3.2 33.1 + - - +
187B GLY* 3.6 10.5 - - - +
307B GLU* 4.7 15.0 - - - +
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Residues in contact with HIS 186 (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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184A PHE* 3.6 29.8 - + + -
185A LYS* 1.3 88.6 - - - +
187A GLY* 1.3 81.8 + - - +
189A VAL* 4.2 9.8 - - + +
250A VAL* 3.7 31.1 - - + +
304A TYR* 3.7 14.1 - + + -
305A PRO 3.1 13.5 - - - +
306A TYR 4.9 0.2 - - - -
92B ASP* 6.1 2.8 - - - +
307B GLU* 5.8 0.3 - - - +
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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