Contacts of the strand formed by residues 198 - 207 (chain A) in PDB entry 1RFV
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 TYR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A LEU 5.1 2.3 - - - +
192A SER* 3.0 29.4 + - - +
194A ARG* 3.8 33.7 - - + -
195A GLY* 3.2 16.0 + - - +
196A SER 4.4 4.3 - - - +
197A ASP* 1.3 87.2 - - + +
199A LEU* 1.3 59.9 + - - +
200A MET 3.9 0.3 + - - -
222A GLU* 4.2 16.6 - - + -
223A MET 3.3 9.6 - - - +
224A HIS* 3.6 42.2 - + + -
225A LYS* 4.4 4.4 - - - -
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Residues in contact with LEU 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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186A THR 6.0 0.2 - - - +
187A SER* 4.0 23.6 - - - -
188A SER 3.9 20.2 - - - +
192A SER* 4.2 1.1 - - - -
197A ASP 4.1 0.8 + - - -
198A TYR* 1.3 72.8 - - - +
200A MET* 1.3 60.7 + - - +
221A MET 3.5 1.0 - - - +
222A GLU* 3.2 6.1 - - - -
223A MET* 2.6 51.1 + - + +
225A LYS* 3.8 26.5 - - + -
401A ADP 4.2 43.7 - - + +
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Residues in contact with MET 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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165A GLN* 2.9 45.8 - - + +
185A ILE 4.5 0.2 - - - +
186A THR 5.1 0.2 - - - -
187A SER* 3.6 4.7 - - - -
188A SER* 3.0 42.8 + - - +
190A LEU* 3.8 34.7 + - + +
191A LEU 4.6 7.4 - - - +
192A SER* 3.9 15.0 - - - +
193A PRO* 4.9 7.2 - - + -
198A TYR 3.9 1.2 + - - -
199A LEU* 1.3 76.3 - - - +
201A ALA* 1.3 65.1 + - - +
202A LEU* 4.3 7.4 - - + +
220A ARG* 2.9 33.2 - - + +
221A MET 3.4 7.9 - - - +
222A GLU* 4.7 3.4 - - - +
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Residues in contact with ALA 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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184A VAL* 5.5 2.2 - - + -
185A ILE* 3.3 14.8 - - - +
186A THR* 3.8 15.9 - - - +
199A LEU 4.0 0.2 + - - -
200A MET* 1.3 74.3 - - - +
202A LEU* 1.3 64.9 + - - +
220A ARG* 3.5 4.3 - - - +
221A MET* 2.8 50.0 + - + +
223A MET* 3.9 21.8 - - + -
237A PHE* 6.1 1.3 - - + -
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Residues in contact with LEU 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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165A GLN* 4.3 11.2 - - + +
168A ALA* 3.4 33.4 - - + -
169A LEU* 4.8 0.9 - - + -
172A MET* 3.5 21.7 - - + +
183A VAL 4.1 0.2 - - - +
184A VAL* 3.4 6.6 - - - +
185A ILE* 2.8 45.4 + - + +
188A SER* 5.5 2.2 - - - +
190A LEU* 4.9 12.1 - - + -
200A MET* 4.3 13.5 - - + -
201A ALA* 1.3 76.3 - - - +
203A GLY* 1.3 58.9 + - - +
219A ILE* 3.5 13.5 - - - +
220A ARG* 3.9 23.1 - - + -
221A MET* 5.0 2.5 - - - -
312A LEU* 4.0 13.5 - - + -
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Residues in contact with GLY 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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172A MET* 4.2 4.9 - - - +
183A VAL 3.5 6.3 - - - -
184A VAL* 4.3 7.2 - - - -
202A LEU* 1.3 76.8 - - - +
204A SER* 1.3 63.0 + - - -
218A ARG* 3.2 5.0 - - - +
219A ILE* 2.8 46.0 + - - +
221A MET* 5.4 0.9 - - - -
252A LEU* 3.7 11.4 - - - -
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Residues in contact with SER 204 (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 MET* 3.9 22.6 - - - +
173A ASP* 4.8 0.7 + - - -
176A HIS* 2.7 31.4 + - - -
182A THR* 3.4 3.1 - - - +
183A VAL* 2.8 37.9 + - - +
203A GLY* 1.3 76.0 - - - -
205A GLN* 1.3 61.7 + - - +
216A THR* 3.6 15.8 - - - +
217A GLN 3.2 6.3 - - - -
218A ARG* 3.9 11.6 + - - +
252A LEU* 3.5 4.4 - - - +
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Residues in contact with GLN 205 (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 HIS* 4.2 1.1 - - - -
181A ASP* 3.2 5.1 - - + +
182A THR* 3.5 23.1 + - - +
204A SER* 1.3 76.6 + - - +
206A ARG* 1.3 65.9 + - - +
207A THR* 3.5 18.6 + - - +
215A VAL 3.7 0.3 - - - +
216A THR* 3.4 4.0 - - - -
217A GLN* 2.8 40.2 + - + +
245A THR* 6.2 2.4 - - - +
249A PRO 3.3 21.9 + - - -
250A ASN* 3.9 12.0 + - - +
252A LEU* 3.5 42.6 + - + +
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Residues in contact with ARG 206 (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* 3.3 38.2 + - - +
176A HIS* 3.5 38.8 - - + +
177A SER* 4.2 13.3 - - - +
181A ASP* 2.7 36.3 + - - +
205A GLN* 1.3 72.5 - - - +
207A THR* 1.3 61.9 + - - +
208A ARG* 3.5 34.8 + - - +
214A VAL* 4.1 22.3 - - + +
215A VAL 4.1 2.0 - - - -
216A THR* 3.4 23.3 + - + +
218A ARG* 5.3 0.8 - - - +
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Residues in contact with THR 207 (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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205A GLN* 3.9 21.7 + - - +
206A ARG* 1.3 70.9 - - - +
208A ARG* 1.3 65.9 + - - +
213A SER 3.9 0.2 - - - +
214A VAL* 4.9 1.1 - - - -
215A VAL* 2.7 60.7 + - + +
217A GLN* 5.7 2.4 + - - +
250A ASN* 3.5 31.6 + - + +
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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