Contacts of the strand formed by residues 243 - 253 (chain A) in PDB entry 4LAX
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 LEU 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TYR 3.6 4.5 - - - +
178A TYR* 4.0 12.3 - - + -
183A PHE* 4.0 12.3 - - + -
201A PRO* 4.5 1.3 - - + -
219A VAL 4.5 0.4 - - - -
220A TYR* 3.5 5.4 - - - +
221A LEU* 2.8 37.5 + - + +
226A ALA* 3.6 27.1 - - + -
227A PHE* 3.7 28.3 - - + -
237A ILE* 3.9 28.7 - - + -
241A ALA* 4.1 3.4 - - + +
242A GLU* 1.3 84.4 - - - +
244A LYS* 1.3 61.6 - - - +
245A TYR* 4.0 26.2 - - + +
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Residues in contact with LYS 244 (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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175A GLU 3.8 0.5 - - - +
176A GLY* 3.5 1.7 - - - -
177A TYR* 2.8 68.0 + - + +
180A ASP* 2.9 29.1 + - - -
218A ILE* 3.7 22.8 - - + +
219A VAL 3.4 4.3 - - - -
220A TYR* 3.4 34.0 + - + +
243A LEU* 1.3 76.0 - - - +
245A TYR* 1.3 64.6 + - - +
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Residues in contact with TYR 245 (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 LEU* 4.1 19.5 - - + -
175A GLU 3.2 7.0 - - - -
176A GLY* 3.5 21.3 - - - -
183A PHE* 3.3 27.2 - + - -
184A ASP* 4.7 4.0 + - - -
199A ASP 4.8 1.9 + - - -
200A LEU* 5.3 1.1 - - + -
201A PRO* 3.2 39.2 - - + +
204A LEU* 3.8 36.3 - - + -
217A SER 3.8 0.9 - - - +
218A ILE* 3.2 7.4 - - - +
219A VAL* 2.8 43.5 + - + +
221A LEU* 3.8 20.2 - - + -
227A PHE* 4.0 3.6 - - - -
243A LEU* 4.0 17.7 - - + +
244A LYS* 1.3 79.4 - - - +
246A GLU* 1.3 57.9 - - - +
247A LEU* 4.0 7.3 + - + +
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Residues in contact with GLU 246 (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 GLN* 5.3 0.2 - - - +
173A ALA 3.8 1.0 - - - +
174A LEU* 3.4 4.2 - - - +
175A GLU* 2.9 58.0 + - + +
177A TYR* 4.8 15.1 + - + -
216A HIS* 2.7 40.4 + - + +
217A SER 3.5 5.2 - - - +
218A ILE* 4.1 22.5 - - + +
244A LYS 4.3 0.2 - - - -
245A TYR* 1.3 71.4 - - - +
247A LEU* 1.3 59.1 + - - +
248A HIS* 4.8 5.4 + - + -
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Residues in contact with LEU 247 (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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172A VAL* 4.9 7.9 - - + -
173A ALA 3.4 3.8 - - - +
174A LEU* 3.7 26.5 - - + -
204A LEU* 3.5 39.0 - - + -
207A ALA* 5.0 1.8 - - + -
208A ILE* 4.4 16.6 - - + -
211A MET* 3.8 29.6 - - + +
215A GLU 3.6 1.4 - - - +
216A HIS* 3.5 5.0 - - - -
217A SER* 2.9 37.8 + - - +
219A VAL* 3.8 20.6 - - + -
245A TYR* 4.3 6.3 - - + +
246A GLU* 1.3 76.6 - - - +
248A HIS* 1.3 63.9 + - - +
249A LEU 4.2 0.2 - - - -
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Residues in contact with HIS 248 (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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172A VAL* 3.3 7.9 - - - +
173A ALA* 2.8 46.8 + - + +
175A GLU* 5.3 7.3 + - - -
211A MET* 4.3 1.1 - - - -
214A GLY 5.5 2.9 - - - -
215A GLU 3.4 6.1 - - - +
216A HIS* 3.3 51.8 + + + -
246A GLU* 4.8 7.5 + - + -
247A LEU* 1.3 75.6 + - - +
249A LEU* 1.3 60.0 + - - +
250A LYS* 3.6 32.4 + - + +
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Residues in contact with LEU 249 (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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164A PRO* 3.7 7.9 - - + -
170A VAL* 4.0 14.4 - - + -
171A GLU 3.8 6.7 - - - +
172A VAL* 3.8 16.4 - - + -
208A ILE* 4.4 4.9 - - + +
211A MET* 3.6 44.1 - - + +
212A GLU 3.5 24.9 - - - +
213A LYS* 4.4 1.8 - - - -
214A GLY* 2.7 35.7 + - - -
215A GLU 3.1 8.7 + - - -
248A HIS* 1.3 71.7 - - - +
250A LYS* 1.3 55.5 + - - +
251A SER 3.7 22.4 - - - +
252A PHE* 3.7 21.5 - - + -
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Residues in contact with LYS 250 (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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171A GLU* 2.8 38.9 + - + +
172A VAL 4.8 0.7 - - - -
173A ALA* 4.4 17.9 - - + +
187A GLU* 5.6 4.7 - - - +
213A LYS* 3.6 17.1 - - - +
214A GLY* 4.7 4.5 + - - +
248A HIS* 3.9 35.9 - - + +
249A LEU* 1.3 76.1 - - - +
251A SER* 1.3 62.1 + - - +
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Residues in contact with SER 251 (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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170A VAL* 3.5 0.2 - - - -
171A GLU* 2.8 56.3 + - - +
213A LYS* 4.1 23.8 - - - -
249A LEU* 3.6 4.8 - - - +
250A LYS* 1.3 81.2 - - - +
252A PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 252 (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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162A ALA* 3.5 34.3 - - + -
163A LYS 3.6 15.9 - - - -
164A PRO* 3.9 15.7 - - + -
168A ALA* 5.0 0.4 - - + -
169A ILE 3.2 13.2 - - - +
170A VAL* 3.7 16.4 - - + -
213A LYS* 3.8 33.7 - - + +
249A LEU* 3.7 23.3 - - + -
251A SER* 1.3 81.6 - - - +
253A GLU* 1.3 73.7 + - - +
254A LYS* 3.7 25.4 - - + -
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Residues in contact with GLU 253 (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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168A ALA* 3.4 3.5 - - - -
169A ILE* 2.9 39.1 + - + +
189A ARG* 6.0 3.8 - - - +
252A PHE* 1.3 81.6 - - - +
254A LYS* 1.3 68.5 + - - +
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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