Contacts of the strand formed by residues 253 - 260 (chain A) in PDB entry 4GB1
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 GLN 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A TRP* 2.8 40.1 + - - +
221A ALA* 4.2 7.7 - - + +
244A THR* 3.2 4.7 - - - +
245A ASP 2.8 39.9 + - - +
252A ALA* 1.3 75.7 - - - +
254A TYR* 1.3 64.1 + - - +
255A ARG* 5.5 1.5 + - + -
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Residues in contact with TYR 254 (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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242A VAL* 5.0 1.3 - - + -
243A MET 3.2 7.4 - - - +
244A THR* 3.9 4.9 - - + +
251A GLN* 3.2 16.5 + - - -
252A ALA* 3.3 39.7 + - + -
253A GLN* 1.3 79.3 - - - +
255A ARG* 1.3 61.2 + - - +
269A ASP* 3.6 2.1 - - - +
270A ILE* 2.7 65.0 + - + -
272A PHE* 3.7 22.7 - + + -
275A GLY 2.7 21.7 + - - -
276A HIS* 3.1 9.7 - + - -
277A ILE* 3.2 54.3 - - + -
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Residues in contact with ARG 255 (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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220A TRP* 3.3 58.5 - - + +
241A TRP 3.7 0.2 - - - +
242A VAL* 3.3 5.2 - - - +
243A MET* 2.8 36.3 + - - +
253A GLN* 5.5 0.8 + - + -
254A TYR* 1.3 79.7 - - - +
256A ILE* 1.3 65.3 + - - +
257A TYR* 3.5 37.8 + - + -
267A GLN* 3.8 18.7 - - - +
268A THR 3.2 12.3 - - - +
269A ASP* 2.9 27.7 + - + +
270A ILE* 3.9 3.8 - - - -
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Residues in contact with ILE 256 (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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240A TYR* 5.0 1.8 - - + -
241A TRP 3.5 8.7 - - - +
242A VAL* 4.6 1.1 - - + +
255A ARG* 1.3 75.5 - - - +
257A TYR* 1.3 67.7 + - - +
267A GLN* 3.3 7.9 - - - +
268A THR* 2.9 47.3 + - - +
270A ILE* 3.6 21.5 - - + -
305A LEU* 4.4 0.9 - - + -
307A ILE* 3.5 50.0 - - + -
312A LEU* 3.7 23.6 - - + +
314A TYR* 4.1 24.5 - - + -
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Residues in contact with TYR 257 (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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217A VAL* 3.2 35.5 - - + +
220A TRP* 3.8 8.6 - + - -
240A TYR* 3.2 7.1 - - - +
241A TRP* 2.9 58.4 + + + +
243A MET* 3.7 33.0 - - + -
255A ARG* 3.5 36.7 + - + -
256A ILE* 1.3 78.5 - - - +
258A LYS* 1.3 60.7 + - - +
264A ILE* 4.4 14.8 - - + -
266A GLY 3.7 4.7 - - - -
267A GLN* 3.3 45.1 + - + -
312A LEU* 5.0 0.2 - - - -
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Residues in contact with LYS 258 (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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238A ASP* 3.3 27.3 + - + -
239A CYS 3.4 3.4 - - - +
240A TYR* 3.1 42.9 + - + -
241A TRP* 4.2 1.1 - - - -
257A TYR* 1.3 75.7 - - - +
259A ALA* 1.3 54.2 + - - +
264A ILE* 3.6 3.0 - - - +
265A ILE* 2.7 50.5 + - + +
266A GLY* 2.8 20.0 + - - +
310A PRO* 3.0 21.9 + - - +
311A ASP* 5.2 0.2 - - - +
312A LEU* 3.8 22.4 - - + -
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Residues in contact with ALA 259 (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 MET* 3.9 17.0 - - - -
207A ILE* 5.4 0.4 - - + -
237A GLY 3.9 0.7 - - - +
238A ASP* 3.2 6.5 - - - +
239A CYS* 2.7 41.4 + - - +
241A TRP* 3.6 25.5 - - + -
258A LYS* 1.3 74.6 - - - +
260A ASN* 1.3 61.7 + - - +
262A GLY 4.5 4.5 - - - +
263A ARG 3.3 21.1 - - - +
264A ILE* 4.3 1.6 - - + +
265A ILE* 4.3 3.1 - - - -
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Residues in contact with ASN 260 (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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84A TYR* 3.4 20.6 + - - -
236A GLN 5.4 0.2 + - - -
237A GLY* 3.4 14.3 + - - -
238A ASP* 3.1 24.7 + - - +
259A ALA* 1.3 72.2 - - - +
261A GLN* 1.3 84.1 + - - +
262A GLY 3.1 0.9 - - - -
263A ARG* 2.9 24.5 + - - +
265A ILE* 3.7 21.0 - - + +
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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