Contacts of the strand formed by residues 215 - 224 (chain A) in PDB entry 1LHP
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 VAL 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLN 3.6 0.7 - - - +
206A ARG* 3.6 1.1 - - - -
207A THR* 2.8 64.3 + - - +
208A ARG* 4.9 4.7 - - + -
213A SER 3.4 5.8 + - - +
214A VAL* 1.3 71.9 - - - +
216A THR* 1.3 71.3 + - - +
217A GLN* 4.8 4.0 - - + +
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Residues in contact with THR 216 (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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173A ASP* 4.9 0.2 - - - +
204A SER* 3.6 23.3 - - - +
205A GLN 3.5 9.6 - - - +
206A ARG* 2.8 33.0 + - + +
214A VAL 3.7 6.5 + - - -
215A VAL* 1.3 83.6 - - - +
217A GLN* 1.3 62.2 + - - +
218A ARG* 3.9 29.7 + - + +
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Residues in contact with GLN 217 (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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203A GLY 3.9 0.3 - - - +
204A SER* 3.4 3.1 - - - -
205A GLN* 2.9 47.2 + - + +
207A THR* 5.6 4.9 - - + -
215A VAL* 4.1 4.4 + - + -
216A THR* 1.3 72.8 - - - +
218A ARG* 1.3 66.0 + - - +
219A ILE* 3.2 32.1 - - - +
250A ASN 4.9 3.4 - - - +
251A ASN* 4.1 6.5 - - - +
252A LEU* 3.4 30.7 + - - +
253A LYS* 3.5 11.5 + - - +
311A VAL* 4.2 19.0 - - + +
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Residues in contact with ARG 218 (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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169A LEU* 4.0 35.9 + - + +
172A MET* 6.4 0.4 - - - +
173A ASP* 2.6 43.4 + - - -
203A GLY 3.3 7.0 - - - +
204A SER* 4.1 16.0 + - - +
206A ARG* 5.1 1.2 - - - +
216A THR* 3.9 22.2 + - + +
217A GLN* 1.3 76.9 - - - +
219A ILE* 1.3 69.7 + - - +
311A VAL* 3.5 7.3 - - - +
312A LEU* 2.9 48.3 + - + +
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Residues in contact with ILE 219 (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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169A LEU* 5.9 0.2 - - - +
202A LEU* 3.5 8.7 - - - +
203A GLY* 2.8 46.1 + - - +
217A GLN* 3.2 31.9 - - - +
218A ARG* 1.3 75.8 - - - +
220A ARG* 1.3 62.4 + - - +
221A MET* 4.1 9.2 - - + -
252A LEU* 3.8 29.4 - - + +
253A LYS* 4.1 14.4 - - + -
256A CYS* 3.9 24.7 - - + -
309A ALA* 4.3 10.8 - - + -
310A THR 3.3 13.5 - - - +
311A VAL* 4.4 4.5 - - + -
312A LEU* 3.9 5.4 - - - +
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Residues in contact with ARG 220 (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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165A GLN* 2.7 36.4 + - - +
193A PRO* 4.3 9.7 - - - +
194A ARG* 3.0 31.9 - - - +
200A MET* 3.2 35.4 - - + -
201A ALA 3.3 10.8 - - - +
202A LEU* 3.9 9.9 - - + -
219A ILE* 1.3 76.1 - - - +
221A MET* 1.3 71.0 + - - +
222A GLU* 3.4 16.8 + - - +
309A ALA* 3.4 0.9 - - - -
310A THR* 3.1 58.6 + - + +
312A LEU* 4.1 19.3 - - + +
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Residues in contact with MET 221 (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 VAL* 5.5 4.9 - - + -
200A MET* 3.4 5.5 - - - +
201A ALA* 2.8 52.5 + - + +
203A GLY 5.5 2.9 - - - +
219A ILE* 4.1 9.6 - - + -
220A ARG* 1.3 79.8 - - - +
222A GLU* 1.3 67.4 + - - +
237A PHE* 5.9 1.6 - - + -
256A CYS* 3.3 49.1 - - + +
257A GLU* 4.4 3.1 - - - -
260A VAL* 3.7 31.6 - - + -
307A VAL* 5.1 6.7 - - + -
308A GLN 4.9 3.6 - - - +
309A ALA* 3.5 24.7 - - + +
310A THR* 5.8 0.2 - - - -
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Residues in contact with GLU 222 (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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192A SER* 3.0 25.2 - - - +
193A PRO* 3.5 15.8 - - - +
194A ARG* 2.8 36.3 - - + +
198A TYR* 4.0 18.5 - - + +
199A LEU 3.2 8.5 - - - +
200A MET* 4.2 2.1 - - - +
220A ARG* 3.4 27.1 + - - +
221A MET* 1.3 85.1 - - - +
223A MET* 1.3 61.1 + - - +
260A VAL* 5.9 0.9 - - - -
307A VAL* 4.3 16.5 - - - +
308A GLN 5.4 1.8 + - - -
310A THR* 6.0 3.4 - - + -
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Residues in contact with MET 223 (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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198A TYR* 3.7 3.6 - - - -
199A LEU* 2.6 49.5 + - + +
222A GLU* 1.3 75.6 - - - +
224A HIS* 1.3 80.0 + - - +
225A LYS* 5.3 1.8 - - - -
226A VAL* 4.3 11.0 - - + +
260A VAL* 4.3 27.1 - - + +
263A MET* 4.9 6.1 - - + -
264A HIS* 4.4 37.2 - - + -
267A LEU* 3.9 25.8 - - + -
307A VAL* 5.1 6.5 - - + -
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Residues in contact with HIS 224 (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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197A ASP* 3.6 37.8 + - + +
198A TYR* 3.5 33.7 - + + -
223A MET* 1.3 93.9 - - - +
225A LYS* 1.3 95.3 + - + +
226A VAL* 4.3 2.4 - - - +
264A HIS* 5.8 3.2 - - + -
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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