Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 2G9A
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A SER* 2.5 25.3 + - - -
189A SER* 3.5 23.8 - - - -
190A SER 2.9 24.1 + - - +
191A TYR* 4.0 2.1 + - - -
193A GLY* 3.3 33.2 - - - +
194A LEU 3.6 8.7 - - - +
195A CYS* 3.9 15.9 - - - +
215A PRO 3.9 3.6 - - - +
216A PRO* 1.3 74.4 - - - +
218A SER* 1.3 53.2 + - - +
219A PHE 3.6 9.9 - - - +
231A ALA* 4.5 4.5 - - + -
232A ALA 3.4 15.3 - - - +
233A THR* 4.2 8.5 - - + -
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Residues in contact with SER 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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175A SER* 3.2 25.0 - - - +
191A TYR* 5.4 1.3 - - - -
216A PRO 3.7 1.4 + - - -
217A VAL* 1.3 71.6 - - - +
219A PHE* 1.3 59.9 + - - +
232A ALA* 2.7 27.0 + - - +
233A THR 3.8 1.2 + - - -
234A LEU* 3.7 31.9 - - - +
257A ASN* 3.8 5.8 + - - -
260A TYR 4.0 0.7 - - - -
261A CYS* 3.6 39.5 - - - +
262A ILE 4.9 0.2 - - - -
2B ARG* 4.8 0.2 + - - -
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Residues in contact with PHE 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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175A SER* 4.1 1.3 + - - -
176A ALA* 4.1 11.2 - - + -
189A SER* 4.0 5.2 - - - -
217A VAL* 3.6 3.6 - - - +
218A SER* 1.3 82.1 - - - +
220A VAL* 1.3 87.3 + - - +
221A LYS* 3.7 31.2 - - + -
230A LEU* 4.5 6.1 - - + -
231A ALA* 3.2 4.9 - - - +
232A ALA* 2.6 45.4 + - + +
262A ILE 3.6 13.7 - - - +
263A PHE* 3.7 35.7 - + + -
264A ALA* 3.3 45.8 - - + -
2B ARG* 5.5 4.0 - - - -
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Residues in contact with VAL 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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176A ALA* 3.5 15.6 - - + +
177A VAL 4.9 0.2 - - - +
178A HIS* 4.4 6.6 - - - +
187A VAL* 3.4 19.1 - - + +
188A SER* 3.8 5.6 - - - -
189A SER* 3.2 37.5 - - - +
195A CYS* 3.9 13.2 - - - -
219A PHE* 1.3 91.2 - - - +
221A LYS* 1.3 69.2 + - - +
229A ILE* 3.1 29.6 - - + -
230A LEU 3.0 9.0 - - - +
231A ALA* 4.4 0.4 - - + -
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Residues in contact with LYS 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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178A HIS* 3.7 31.4 - - + +
187A VAL* 4.3 1.3 - - - -
219A PHE* 3.7 18.8 - - + -
220A VAL* 1.3 80.6 - - - +
222A PHE* 1.3 75.4 + - - +
229A ILE* 3.2 6.7 - - - -
230A LEU* 2.7 35.3 + - + +
263A PHE* 6.1 1.2 - - - +
264A ALA 3.7 23.0 + - - +
265A ASN* 3.9 16.4 + - - +
266A PHE* 4.1 19.4 - - + +
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Residues in contact with PHE 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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178A HIS* 3.0 33.0 + + + +
179A PHE 3.9 9.0 - - - +
180A ASN* 4.0 18.6 - - + -
181A ARG 5.8 0.2 - - - +
185A LEU* 3.8 32.1 - - + -
186A ILE 4.5 1.1 - - - -
187A VAL* 3.4 47.3 - - + -
197A ILE* 4.6 6.7 - - + -
221A LYS* 1.3 89.0 - - - +
223A SER* 1.3 69.1 + - - +
224A PRO* 4.0 0.3 - - - +
226A GLY* 3.9 23.3 - - - -
228A TYR 3.4 4.0 - - - -
229A ILE* 3.3 24.0 - - + -
243A TYR* 4.2 14.8 - + - -
266A PHE* 3.6 3.0 - - - -
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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