Contacts of the strand formed by residues 208 - 213 (chain A) in PDB entry 1LC7
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 ILE 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ALA* 4.2 13.5 - - + -
182A LEU* 3.3 15.5 - - + +
184A LEU* 4.0 23.3 - - + -
198A PHE* 3.9 22.2 - - + -
202A LEU* 3.5 31.8 - - + +
205A ASN* 3.2 33.4 + - + +
207A HIS* 1.3 104.6 - - + +
209A TRP* 1.3 66.6 + - - +
210A VAL* 4.4 2.0 - - + -
230A ASN* 3.0 19.8 - - - +
231A SER 4.9 0.2 + - - -
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Residues in contact with TRP 209 (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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92A VAL* 4.1 18.6 - - + -
96A LEU* 3.7 24.0 - - + +
181A ASN* 3.6 25.4 + - + -
182A LEU 2.8 11.9 + - - +
183A ILE* 3.4 14.8 - - + +
184A LEU* 2.8 27.2 + - - +
206A PRO 4.3 2.5 + - - -
207A HIS 3.7 12.4 + - - -
208A ILE* 1.3 79.6 - - - +
210A VAL* 1.3 63.2 + - - +
211A LEU* 6.0 1.8 - - + -
228A LEU* 5.3 9.9 - - + -
229A VAL 3.6 7.4 - - - +
230A ASN* 3.3 37.3 + - + -
235A ALA* 3.6 26.2 - - + -
236A MET* 3.4 25.1 - - - -
239A MET* 3.5 29.8 - - + -
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Residues in contact with VAL 210 (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 LEU* 3.5 5.6 - - + +
186A GLU* 3.3 34.1 - - + +
198A PHE* 4.2 18.2 - - + -
199A ILE* 3.9 25.4 - - + +
202A LEU* 4.1 21.8 - - + -
208A ILE* 4.4 2.7 - - + -
209A TRP* 1.3 77.5 - - - +
211A LEU* 1.3 65.2 + - - +
212A ARG* 3.8 16.3 + - + -
227A TYR 3.9 0.3 - - - +
228A LEU* 3.3 5.7 - - - +
229A VAL* 2.9 36.7 + - + +
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Residues in contact with LEU 211 (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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85A GLU* 3.5 17.5 - - - +
88A SER* 3.7 35.4 - - - +
89A ILE* 3.8 27.6 - - + -
92A VAL* 4.8 7.0 - - + -
111A TYR* 4.9 4.7 - - + -
151A PHE* 5.5 0.4 - - + -
183A ILE* 3.7 31.2 - - + -
184A LEU 2.9 10.1 + - - +
185A ASP* 4.0 17.5 - - + +
186A GLU* 2.9 25.6 + - - +
209A TRP* 5.9 1.6 - - + -
210A VAL* 1.3 76.2 - - - +
212A ARG* 1.3 65.7 + - - +
227A TYR 3.7 1.6 - - - -
228A LEU* 4.3 9.9 - - + -
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Residues in contact with ARG 212 (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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71A HIS* 5.2 5.3 - - - -
72A HIS* 4.0 19.0 - - - -
85A GLU* 3.1 14.2 - - - +
186A GLU* 3.0 39.6 + - - -
189A ILE* 3.5 18.1 - - - +
190A ASP* 3.3 25.9 + - - +
196A THR 4.4 10.1 + - - -
199A ILE* 4.0 16.8 - - + +
210A VAL* 3.8 11.2 - - + +
211A LEU* 1.3 82.6 - - - +
213A SER* 1.3 59.1 + - - +
226A GLY* 3.2 2.6 - - - -
227A TYR* 2.8 73.3 + - + +
229A VAL* 4.9 0.2 - - + -
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Residues in contact with SER 213 (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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85A GLU* 3.3 13.3 + - - -
187A ALA* 4.3 22.2 + - - +
190A ASP* 4.0 16.8 + - - +
212A ARG* 1.3 79.0 - - - +
214A LEU* 1.3 68.1 + - - +
215A THR* 3.0 14.9 + - - -
216A LYS* 4.1 8.3 + - - +
217A PHE* 5.1 3.1 + - - +
225A LEU 3.9 4.5 - - - -
226A GLY* 4.1 0.9 - - - -
227A TYR* 5.1 0.7 - - - -
800A PO4 2.6 30.2 + - - -
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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