Contacts of the strand formed by residues 213 - 222 (chain C) in PDB entry 2GD4
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 LEU 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C THR* 6.1 1.1 - - + -
146C LEU* 4.2 24.5 - - + -
147C PHE 3.1 30.5 - - - +
148C GLY* 4.6 3.6 - - - +
154C PHE* 5.8 3.1 - - + -
170C LEU* 4.9 7.9 - - + -
211C THR 3.6 0.6 - - - -
212C VAL* 1.3 85.3 - - + +
214C VAL* 1.3 66.6 + - - +
215C LEU* 4.8 4.7 - - + -
351C LEU* 4.0 14.4 - - + -
354C ILE* 5.2 9.2 - - + -
362C LEU* 4.8 14.4 - - + -
363C TYR 3.0 26.2 - - - +
364C VAL* 3.4 23.2 - - + -
365C SER* 2.7 30.7 + - - -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LEU* 3.9 1.9 - - - +
147C PHE* 3.0 55.7 + - + +
175C PHE* 4.3 10.5 - - + -
186C ILE* 4.7 7.4 - - + -
202C ILE* 4.9 0.7 - - + -
206C ALA 5.8 0.9 - - - +
207C ILE* 4.7 6.1 - - + -
211C THR* 3.6 22.7 - - + -
213C LEU* 1.3 79.3 - - - +
215C LEU* 1.3 66.2 + - - +
216C VAL* 3.7 9.1 + - + +
364C VAL* 4.6 0.2 - - - -
365C SER* 4.5 1.3 - - - -
366C ASP* 3.1 26.9 - - + +
368C PHE* 4.5 12.3 - - + -
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 4.7 6.3 - - + -
87C PHE* 3.4 54.5 - - + +
90C THR* 4.2 12.6 - - - +
146C LEU* 3.2 31.9 - - + -
213C LEU* 4.8 4.9 - - + -
214C VAL* 1.3 73.3 - - - +
216C VAL* 1.3 62.2 + - - +
217C ASN* 4.2 7.4 - - - +
343C LEU* 5.4 0.9 - - + -
364C VAL* 4.0 22.4 - - + -
366C ASP 2.8 9.1 + - - +
367C ALA* 3.6 15.0 - - + +
368C PHE* 2.5 35.0 + - - +
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ALA 4.9 1.8 - - - +
144C ASN* 2.9 4.8 - - - +
145C ARG 2.6 45.6 + - - +
146C LEU* 5.0 0.6 - - - +
147C PHE* 3.5 33.9 - - + -
166C TYR* 4.0 1.3 + - - -
186C ILE* 4.8 0.9 - - + -
189C TRP* 5.9 1.1 - - + -
190C VAL* 4.7 7.9 - - + -
201C VAL* 3.6 38.1 - - + -
202C ILE* 4.3 18.6 - - + -
214C VAL* 4.0 6.7 - - + +
215C LEU* 1.3 81.4 - - - +
217C ASN* 1.3 61.9 + - - +
218C THR* 4.6 4.0 - - + -
368C PHE* 3.4 3.6 - - + +
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Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C SER* 4.4 11.7 - - - +
83C ILE* 4.2 7.1 - - - +
86C ALA* 3.1 30.9 - - + +
87C PHE* 5.5 0.2 - - - -
144C ASN* 3.1 19.7 - - + +
166C TYR* 4.1 3.3 + - - +
215C LEU* 4.4 8.5 - - - +
216C VAL* 1.3 83.0 - - - +
218C THR* 1.3 69.8 + - - +
331C LEU* 3.8 12.5 - - - +
368C PHE 3.1 3.4 + - - +
369C HIS* 2.9 45.9 + - - +
370C LYS 3.1 13.5 + - - -
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Residues in contact with THR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C SER* 3.3 3.8 - - - -
143C ALA* 2.3 71.6 + - - +
144C ASN* 4.0 1.5 - - - +
190C VAL* 4.0 5.5 - - + +
194C THR* 4.5 1.0 - - - +
198C ILE* 4.0 10.9 - - + +
201C VAL* 3.4 24.7 - - + -
216C VAL* 4.6 1.8 - - + -
217C ASN* 1.3 87.0 - - - +
219C ILE* 1.3 64.9 + - - +
369C HIS* 5.1 0.9 - - - -
370C LYS* 3.0 36.6 - - + -
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Residues in contact with ILE 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PHE* 5.2 0.2 - - - -
79C SER* 3.3 30.3 - - - +
81C LEU* 6.2 0.7 - - + -
82C SER* 3.1 29.2 - - - +
140C LEU* 3.2 32.3 - - + -
141C VAL 3.2 8.7 - - - +
142C SER* 4.5 9.6 - - - -
144C ASN* 6.5 0.4 - - - -
194C THR* 6.2 0.2 - - - -
198C ILE* 3.5 8.5 - - - +
218C THR* 1.3 80.9 - - - +
220C TYR* 1.3 72.0 + - - +
369C HIS* 5.2 3.1 - - + -
370C LYS 2.9 7.3 + - - -
371C ALA* 3.3 6.3 - - + +
372C PHE 2.9 26.6 + - - +
421C ILE* 6.0 0.4 - - + -
422C PHE* 3.6 16.6 - - + -
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LYS* 4.5 9.6 - - + -
140C LEU* 3.2 9.5 - - - +
141C VAL* 2.7 51.8 + - + +
197C ARG* 3.6 43.9 + - + -
198C ILE* 3.4 14.6 - - + -
219C ILE* 1.3 74.5 - - - +
221C PHE* 1.3 71.9 + - - +
222C LYS* 3.1 49.2 + - + +
372C PHE* 3.1 46.0 - + - -
374C GLU* 3.7 5.6 + - + +
422C PHE* 5.0 0.2 - - - -
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Residues in contact with PHE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PHE* 5.0 1.1 - - + -
134C ALA* 4.8 10.5 - - + -
138C SER* 4.8 7.0 - - - -
139C LYS 3.5 13.2 - - - -
140C LEU* 3.9 20.4 - - + -
220C TYR* 1.3 80.7 - - - +
222C LYS* 1.3 62.3 + - - +
223C GLY* 3.0 30.1 - - - -
274C PHE* 3.4 35.4 - + - -
279C ILE* 4.6 4.9 - - + -
372C PHE 3.1 9.1 + - - +
373C LEU* 3.6 19.0 - - + +
374C GLU* 3.1 24.9 + - - +
412C ILE* 4.0 13.5 - - + -
421C ILE* 5.9 1.3 - - + -
422C PHE* 3.4 36.8 - + + -
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Residues in contact with LYS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C SER* 3.9 0.5 - - - -
139C LYS* 3.2 30.1 + - + +
220C TYR* 3.1 33.9 + - + +
221C PHE* 1.3 77.4 - - - +
223C GLY* 1.3 69.4 + - - +
374C GLU* 3.0 46.0 + - + +
376C ASN* 3.6 23.1 + - - +
378C GLU* 5.6 5.4 - - + +
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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