Contacts of the strand formed by residues 180 - 188 (chain A) in PDB entry 5E63
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 GLY 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A VAL* 2.8 41.2 + - - +
177A SER 5.3 0.7 - - - +
178A GLY 4.5 0.9 - - - +
179A ASP* 1.3 73.8 - - - +
181A SER* 1.3 67.5 + - - -
182A PHE* 5.6 0.7 - - - -
203A GLN 3.3 9.4 - - - -
204A ILE* 4.1 6.3 - - - -
16E C 4.1 11.1 - - - +
17E A 4.4 0.3 + - - -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 4.9 2.4 - - - +
179A ASP 4.9 1.0 + - - -
180A GLY* 1.3 75.2 - - - -
182A PHE* 1.3 65.8 + - - +
183A LYS* 3.8 13.4 - - - +
201A VAL 3.6 2.1 - - - +
202A PHE* 3.4 6.8 - - - -
203A GLN* 2.6 55.0 + - - +
205A THR* 5.2 1.2 + - - -
16E C 3.4 18.8 - - - +
17E A 2.8 29.6 - - - -
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Residues in contact with PHE 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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176A VAL* 4.1 11.2 - - + -
180A GLY 5.7 0.4 - - - -
181A SER* 1.3 73.8 - - - +
183A LYS* 1.3 62.0 + - - +
201A VAL 3.8 2.7 - - - -
202A PHE* 3.4 34.3 - + - -
249A ILE* 4.6 0.2 - - + -
253A PHE* 4.3 10.3 - + - -
258A ILE* 3.9 30.5 - - + -
262A ALA* 4.8 8.7 - - + -
265A ASP* 4.6 9.3 - - + +
266A TYR* 3.8 38.1 - + + -
269A TRP* 3.6 47.1 - + + +
297A MET* 3.4 19.2 - - + +
298A ASN* 5.9 0.3 + - - -
17E A 4.6 3.2 + - - -
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Residues in contact with LYS 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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181A SER* 4.4 14.8 - - - +
182A PHE* 1.3 75.2 - - - +
184A SER* 1.3 60.6 + - - +
185A ILE* 3.7 16.2 - - + +
199A ILE 3.8 0.2 - - - +
200A LEU* 3.4 3.5 - - - -
201A VAL* 2.7 52.0 + - + +
203A GLN* 3.1 41.5 + - - +
269A TRP* 2.9 19.0 + - - +
17E A 3.7 26.7 + - + +
18E G 3.2 43.5 + - + +
19E G 5.5 0.6 + - - -
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Residues in contact with SER 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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182A PHE 4.0 1.8 + - - -
183A LYS* 1.3 73.2 - - - +
185A ILE* 1.3 64.9 + - - +
186A LEU* 5.1 0.3 - - - +
198A SER* 5.5 0.9 + - - -
199A ILE 3.5 6.2 + - - -
200A LEU* 4.4 4.3 - - - -
269A TRP* 4.9 0.4 - - - -
272A ILE* 3.7 32.0 - - - +
290A ILE* 4.2 9.4 - - - +
294A LYS* 2.9 44.2 + - - +
297A MET* 4.6 9.0 - - - +
18E G 4.3 8.2 + - - +
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Residues in contact with ILE 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 LYS* 3.7 35.2 - - + +
184A SER* 1.3 76.7 + - - +
186A LEU* 1.3 71.4 + - - +
187A LYS* 4.2 4.0 - - + +
197A GLN 3.3 2.1 - - - +
198A SER* 3.6 2.3 + - - -
199A ILE* 2.7 51.3 + - + +
201A VAL* 4.1 20.9 - - + -
294A LYS* 3.8 1.8 - - - +
18E G 4.6 10.1 - - + +
19E G 4.0 38.1 - - + +
20E T 3.7 29.2 - - + -
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Residues in contact with LEU 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 SER* 5.1 0.9 - - - +
185A ILE* 1.3 81.1 - - - +
187A LYS* 1.3 60.6 + - - +
188A LYS 4.0 1.4 + - - -
196A PHE* 4.2 17.2 - - + -
197A GLN 3.3 9.0 - - - +
198A SER* 4.0 10.8 - - - +
287A LEU* 4.2 17.7 - - + -
290A ILE* 4.1 18.4 - - + -
291A ARG* 3.5 42.8 - - + +
294A LYS* 3.7 30.2 - - + +
19E G 3.6 19.5 + - - +
20E T 4.5 0.2 + - - -
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Residues in contact with LYS 187 (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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185A ILE* 4.3 4.7 - - + -
186A LEU* 1.3 73.6 - - - +
188A LYS* 1.3 81.3 + - - +
189A SER* 3.1 4.5 + - - +
196A PHE* 3.2 5.7 - - - -
197A GLN* 2.9 54.5 + - + +
199A ILE* 4.2 7.6 - - + -
3B T 6.0 0.4 - - - -
4B A 3.4 2.2 - - - +
20E T 3.4 52.4 - - + +
21E G 2.5 51.2 + - - +
22E T 2.8 18.8 + - - -
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Residues in contact with LYS 188 (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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186A LEU 4.0 1.2 + - - -
187A LYS* 1.3 88.7 - - - +
189A SER* 1.3 58.3 + - - +
190A GLU* 3.5 28.7 - - - +
195A GLY* 3.0 35.6 + - - +
196A PHE* 3.9 31.0 - - + -
20E T 3.3 24.3 + - - +
22E T 5.9 1.2 - - - +
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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