Contacts of the strand formed by residues 283 - 290 (chain A) in PDB entry 1D2G
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 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY 4.6 3.9 + - - -
138A ASN* 4.0 16.2 - - + -
173A ASP* 3.8 16.4 - - - +
174A HIS 3.6 7.4 - - - +
175A LYS* 3.1 43.7 + - + +
190A LYS 4.0 4.5 - - - -
191A ASN* 3.2 29.8 + - - -
192A ILE* 3.4 56.8 - - + -
193A TYR* 3.9 13.2 - + - +
268A GLY* 3.7 5.2 - - - -
269A ASP* 2.8 26.0 + - - +
281A PRO* 3.7 3.7 - - - +
282A CYS* 1.3 84.4 - - + +
284A PHE* 1.3 64.3 + - - +
285A ILE* 4.0 3.3 + - + -
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Residues in contact with PHE 284 (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* 3.1 3.7 - - - -
174A HIS* 2.7 65.9 + + + +
176A ASN* 3.1 46.0 - - + -
178A ASP* 4.3 7.2 - - - -
247A LEU* 3.3 34.8 - - + -
266A VAL* 4.4 5.4 - - + -
267A LEU 3.5 11.7 - - - +
273A TYR* 3.9 19.7 - + - -
281A PRO* 3.4 29.6 - - + -
283A TYR* 1.3 73.4 - - - +
285A ILE* 1.3 61.9 + - - +
286A HIS* 3.7 9.1 - - - +
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TRP* 3.9 15.7 - - + -
136A LEU* 4.3 5.2 - - + -
171A VAL* 3.8 29.2 - - + -
172A ILE 4.3 3.4 - - - +
173A ASP* 3.8 5.8 - - + -
192A ILE* 4.1 6.3 - - + -
193A TYR* 3.7 24.0 - - - +
265A SER 3.8 0.7 - - - +
266A VAL* 3.4 2.8 - - - -
267A LEU* 2.8 47.6 + - + +
269A ASP 4.1 9.0 - - - +
270A PHE* 3.7 44.9 - - + +
283A TYR* 4.6 2.5 - - + +
284A PHE* 1.3 75.3 - - - +
286A HIS* 1.3 65.6 + - - +
287A VAL* 3.9 1.2 + - + +
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Residues in contact with HIS 286 (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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170A LEU 3.3 4.9 - - - +
171A VAL* 3.4 1.4 - - - -
172A ILE* 2.8 48.7 + - + +
174A HIS* 3.1 29.0 - + - -
247A LEU* 3.6 14.4 - - + +
250A PHE* 3.7 22.2 - + + -
251A THR* 3.4 25.4 - - - -
254A VAL* 4.3 1.1 - - + +
264A HIS* 2.9 26.1 + + + -
265A SER 3.7 4.3 - - - -
266A VAL* 4.2 4.5 - - + +
284A PHE* 3.7 13.8 - - - +
285A ILE* 1.3 79.0 - - - +
287A VAL* 1.3 60.7 + - - +
288A LEU* 3.8 14.1 - - + +
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Residues in contact with VAL 287 (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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47A TRP* 5.2 1.8 - - + -
51A LEU* 4.6 22.9 - - + -
55A HIS* 5.6 3.1 - - + +
169A LEU* 4.7 12.1 - - + -
170A LEU 3.3 5.6 - - - +
171A VAL* 4.5 9.9 - - + +
263A GLN 3.5 4.0 - - - +
265A SER* 3.0 39.2 + - - +
267A LEU* 3.8 32.3 - - + -
285A ILE* 4.4 3.8 - - + +
286A HIS* 1.3 73.9 - - - +
288A LEU* 1.3 70.7 + - - +
289A LYS* 5.2 1.6 - - + +
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Residues in contact with LEU 288 (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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168A GLY 3.8 0.2 - - - +
169A LEU* 3.1 6.2 - - - +
170A LEU* 2.7 48.7 + - + +
172A ILE* 5.6 0.2 - - + -
254A VAL* 3.8 16.2 - - + +
258A PHE* 3.8 32.0 - - + -
262A CYS* 3.8 26.5 - - + -
263A GLN 3.3 4.3 - - - +
264A HIS* 3.4 40.8 - - + +
286A HIS* 3.8 9.0 - - + +
287A VAL* 1.3 95.2 - - - +
289A LYS* 1.3 61.3 + - - +
290A LYS 4.0 0.6 + - - -
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Residues in contact with LYS 289 (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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55A HIS* 3.8 29.0 + - + +
167A GLY* 3.2 26.0 + - - +
168A GLY 3.2 9.9 - - - +
169A LEU* 4.0 12.0 - - + +
258A PHE* 5.1 0.2 - - - -
262A CYS* 3.4 3.1 - - - -
263A GLN* 3.0 62.9 + - + +
287A VAL* 5.2 1.8 - - + +
288A LEU* 1.3 72.7 - - - +
290A LYS* 1.3 72.1 + - - +
291A THR* 3.1 5.1 + - - +
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Residues in contact with LYS 290 (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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161A ALA* 3.3 23.4 + - - +
162A SER* 4.0 9.9 + - - +
164A VAL* 2.9 29.7 + - + +
165A ARG 3.4 20.9 - - - +
166A PRO* 3.8 12.8 - - + -
167A GLY* 2.6 32.1 + - - -
168A GLY 2.7 12.9 + - - +
258A PHE* 3.7 34.3 - - + +
261A ARG 4.8 0.4 - - - +
288A LEU 4.0 1.6 + - - -
289A LYS* 1.3 70.0 - - - +
291A THR* 1.3 60.6 + - - +
292A GLY* 4.2 19.5 - - - +
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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