Contacts of the strand formed by residues 288 - 294 (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 LYS 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ILE* 3.7 6.5 - - - +
284A PRO* 3.8 0.2 - - - +
285A ASN 3.0 31.2 + - - +
286A ASP* 3.2 8.8 - - + +
287A GLY* 1.3 83.2 - - - +
289A VAL* 1.3 65.6 + - - +
290A GLU* 4.1 0.4 - - - -
306A VAL* 3.8 25.8 - - + +
307A ILE 3.5 13.0 - - - +
308A SER* 3.5 28.3 + - - +
310A PRO* 4.4 2.9 - - + -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 3.6 43.1 - - + +
235A ILE* 3.8 10.3 - - + -
240A TYR* 4.0 25.8 - - + +
282A CYS* 3.9 16.8 - - + -
283A TYR 3.9 2.9 - - - +
288A LYS* 1.3 80.1 - - - +
290A GLU* 1.3 63.2 + - - +
291A CYS* 4.0 7.5 + - - -
305A LEU 3.5 1.7 - - - +
306A VAL* 3.2 3.7 - - - -
307A ILE* 2.9 52.3 + - + +
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Residues in contact with GLU 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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282A CYS* 3.0 2.1 - - - -
283A TYR* 2.5 71.9 + - + +
285A ASN* 3.0 40.6 + - + +
288A LYS* 4.6 0.4 - - - +
289A VAL* 1.3 78.6 - - - +
291A CYS* 1.3 59.7 + - - +
305A LEU 3.4 7.9 - - - +
306A VAL* 4.4 18.5 - - + +
360A ARG* 3.2 32.8 + - - +
388A TRP* 3.9 13.5 - - + -
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Residues in contact with CYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 4.2 10.8 - - - -
280A CYS* 3.9 1.1 - - + -
281A SER 3.3 4.9 - - - +
282A CYS* 2.0 45.1 - - - -
289A VAL* 4.2 11.0 - - - -
290A GLU* 1.3 75.8 - - - +
292A VAL* 1.3 65.5 + - - +
293A CYS* 3.6 19.5 - - - -
303A PRO 4.1 0.2 - - - +
304A VAL* 3.3 8.1 - - - +
305A LEU* 3.1 45.3 + - + +
307A ILE* 4.6 1.8 - - - -
388A TRP* 5.5 0.2 - - - -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 2.9 30.7 + - - +
283A TYR* 4.8 0.9 - - + -
291A CYS* 1.3 77.0 - - - +
293A CYS* 1.3 58.3 + - - +
302A ARG* 3.5 36.6 - - + -
303A PRO 3.6 5.2 - - - +
304A VAL* 4.0 15.9 - - + -
319A LEU* 4.5 13.0 - - + -
356A GLY 3.5 6.0 - - - +
357A PHE 4.1 2.0 - - - +
358A GLY* 3.6 43.5 - - - +
388A TRP* 4.3 14.1 - - + -
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Residues in contact with CYS 293 (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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277A ILE* 3.8 11.2 - - + -
278A GLU 3.5 4.0 - - - +
279A GLU 4.1 2.7 - - - -
280A CYS* 2.1 55.6 - - - +
291A CYS* 3.6 14.4 - - - -
292A VAL* 1.3 76.4 - - - +
294A ARG* 1.3 61.8 + - - +
302A ARG* 3.0 32.4 - - - +
303A PRO* 2.9 19.0 + - + +
305A LEU* 3.6 12.3 - - - -
356A GLY 5.4 0.7 - - - -
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Residues in contact with ARG 294 (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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277A ILE* 3.4 4.3 - - - -
278A GLU* 2.7 52.8 + - + +
279A GLU* 2.7 38.6 + - + +
293A CYS* 1.3 73.6 - - - +
295A ASP* 1.3 68.9 + - - +
296A ASN* 2.5 34.2 + - - +
302A ARG* 3.5 17.3 - - - +
303A PRO* 3.7 2.9 - - - -
326A ASP* 4.4 1.6 - - - +
352A TYR* 4.8 6.5 - - - -
353A GLY* 3.2 24.2 + - - +
354A VAL* 3.8 22.8 - - - +
355A LYS* 4.5 4.9 - - - -
376A ARG* 4.2 0.2 - - - +
411A TYR* 3.4 5.5 + - - -
501A 0LP 3.2 45.5 + - - -
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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
------------------------------------------------------------
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