Contacts of the strand formed by residues 194 - 203 (chain A) in PDB entry 4LL1
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 GLU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ARG* 5.2 1.4 + - - -
189A PHE* 4.0 12.0 - - - -
192A GLY 5.4 0.3 - - - +
193A ASP* 1.3 81.4 - - - +
195A ILE* 1.3 63.5 + - - +
196A SER* 3.6 5.1 + - - +
254A SER* 3.7 30.1 + - - -
255A LEU 3.4 9.0 - - - +
256A ARG* 3.6 31.9 + - + +
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Residues in contact with ILE 195 (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 ILE* 3.7 28.5 - - + -
189A PHE* 3.8 35.4 - - + -
194A GLU* 1.3 70.9 - - - +
196A SER* 1.3 62.3 + - - +
197A ILE* 3.8 5.1 + - + +
215A ILE* 4.0 20.0 - - + -
253A LYS 3.6 0.9 - - - +
254A SER* 3.1 4.5 - - - -
255A LEU* 2.8 39.5 + - + +
257A VAL* 3.8 18.6 - - + -
276A LEU* 3.9 13.9 - - + -
294A LEU* 3.4 32.8 - - + -
296A ILE* 5.8 0.2 - - + -
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Residues in contact with SER 196 (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 ARG 4.1 2.6 - - - +
184A ILE* 3.7 20.1 - - - +
185A ASP* 4.6 21.2 + - - +
189A PHE* 5.2 1.8 - - - -
194A GLU* 3.6 6.1 + - - -
195A ILE* 1.3 73.9 - - - +
197A ILE* 1.3 58.4 + - - +
252A GLY* 3.2 24.6 + - - -
253A LYS 3.6 4.0 - - - -
254A SER* 4.2 8.5 - - - -
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Residues in contact with ILE 197 (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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182A ALA* 4.7 0.7 - - + -
183A ARG 3.9 5.6 - - - +
184A ILE* 4.2 2.5 - - + -
195A ILE* 4.0 9.6 - - + +
196A SER* 1.3 79.9 + - - +
198A HIS* 1.3 74.4 + - - +
199A ALA* 4.2 5.8 - - + -
213A ALA* 4.3 17.9 - - + -
237A VAL* 5.1 0.4 - - + -
250A TRP* 3.9 30.6 - - + +
252A GLY 3.1 19.6 + - - -
253A LYS* 2.6 29.2 + - + +
255A LEU* 4.4 12.8 - - + -
276A LEU* 4.2 35.0 - - + -
278A ILE* 4.3 17.3 - - + -
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Residues in contact with HIS 198 (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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181A SER 5.6 0.4 + - - -
182A ALA* 3.3 2.3 - - - -
183A ARG* 2.8 72.8 + - + +
197A ILE* 1.3 72.9 - - - +
199A ALA* 1.3 61.7 + - - +
200A ASP* 4.3 11.0 - - - -
250A TRP 3.4 4.9 - - - -
251A ARG* 3.1 51.3 + - - -
252A GLY 4.5 3.1 - - - +
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Residues in contact with ALA 199 (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 VAL* 4.8 0.7 - - + -
181A SER 3.2 12.1 - - - +
182A ALA* 4.1 11.2 - - + -
197A ILE* 4.2 9.6 - - + -
198A HIS* 1.3 77.3 - - - +
200A ASP* 1.3 71.8 + - - +
201A PHE* 3.7 29.4 - - + -
249A SER* 3.2 0.9 - - - -
250A TRP* 2.8 39.3 + - + +
251A ARG* 3.3 0.9 + - - -
278A ILE* 4.9 1.1 - - + -
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Residues in contact with ASP 200 (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 SER* 4.5 1.4 + - - -
180A VAL* 3.4 3.6 - - - -
181A SER* 2.9 40.4 + - - +
198A HIS* 4.3 10.2 - - - -
199A ALA* 1.3 75.3 - - - +
201A PHE* 1.3 62.8 + - - +
202A GLU* 6.0 0.2 - - - -
248A ALA 3.5 4.5 - - - -
249A SER* 3.1 4.2 + - - -
251A ARG* 2.8 38.8 + - - -
31B TRP* 3.6 41.5 + - + +
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Residues in contact with PHE 201 (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 SER 3.3 4.0 - - - +
180A VAL* 3.4 27.8 - - + -
199A ALA* 3.7 27.6 - - + -
200A ASP* 1.3 74.9 - - - +
202A GLU* 1.3 62.7 + - - +
211A PRO* 3.5 24.9 - - + -
242A ILE* 3.5 24.9 - - + +
247A CYS* 3.1 8.5 - - - +
248A ALA* 2.8 39.7 + - + +
250A TRP* 3.7 37.2 - + - -
278A ILE* 4.2 9.4 - - + -
279A TYR 4.8 0.9 - - - -
280A VAL* 3.7 24.7 - - + -
31B TRP* 4.2 0.9 - - - -
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Residues in contact with GLU 202 (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 ARG* 4.4 4.1 - - + +
178A VAL* 3.3 8.7 - - - +
179A SER* 3.0 47.2 + - - +
200A ASP 6.0 0.4 - - - -
201A PHE* 1.3 74.9 - - - +
203A ASN* 1.3 63.0 + - - +
204A THR* 4.1 10.1 - - + +
209A VAL* 5.4 0.6 - - - +
242A ILE* 5.4 0.4 - - - -
247A CYS* 3.7 15.7 - - - -
31B TRP* 3.1 21.1 - - + +
33B GLY* 2.7 38.4 + - - -
34B PRO* 4.0 4.9 - - - +
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Residues in contact with ASN 203 (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 ARG 3.7 2.2 - - - -
178A VAL* 3.7 5.0 - - + +
202A GLU* 1.3 75.3 - - - +
204A THR* 1.3 53.7 + - - +
205A SER* 2.7 29.9 + - - -
207A ARG 2.8 26.2 + - - -
209A VAL* 3.7 18.3 - - + +
242A ILE* 3.0 32.5 + - + -
243A ILE 3.4 9.8 + - - +
244A SER 3.6 0.2 - - - +
245A GLY* 2.7 34.7 + - - -
246A THR 3.0 18.8 + - - +
247A CYS* 4.7 0.4 - - - -
34B PRO* 4.9 0.2 - - - -
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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