Contacts of the strand formed by residues 334 - 342 (chain A) in PDB entry 4G84
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A MET* 3.4 31.4 - - + -
188A ASP* 3.7 23.3 + - + +
211A VAL* 4.9 1.3 - - + -
212A ASN 3.3 8.1 - - - +
213A ASP* 3.3 7.7 + - - +
301A ASP* 5.5 0.2 - - + -
302A LEU* 4.0 20.0 - - + -
305A LEU* 4.1 7.6 - - + -
331A TYR* 4.4 0.3 - - - -
333A GLY* 1.3 75.2 - - - +
335A ILE* 1.3 62.9 + - - +
336A TYR* 3.7 29.2 - - + -
361A GLY* 3.1 1.8 - - - -
362A ARG* 2.9 33.7 + - - +
380A VAL* 4.5 0.4 - - + -
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Residues in contact with ILE 335 (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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211A VAL* 3.4 4.2 - - - +
212A ASN* 2.8 34.9 + - + +
213A ASP 4.7 1.6 - - - -
214A ARG* 4.3 17.0 - - - +
217A LEU* 4.7 2.2 - - + -
324A LEU* 3.3 33.5 - - + +
326A ARG* 3.9 33.7 - - + +
328A LEU* 4.0 19.3 - - + -
331A TYR* 3.8 23.8 - - + -
333A GLY 3.9 4.3 - - - +
334A VAL* 1.3 80.5 - - - +
336A TYR* 1.3 68.9 + - - +
360A GLY 3.5 10.1 - - - +
361A GLY* 4.1 0.2 - - - -
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Residues in contact with TYR 336 (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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188A ASP 4.6 4.0 - - - -
191A CYS* 3.2 25.3 - - + +
192A LEU* 3.5 38.1 - - + -
195A MET* 3.3 30.1 - - + -
209A VAL* 4.0 3.1 - - + -
210A LYS 3.1 13.0 - - - +
211A VAL* 4.1 5.4 - - + -
324A LEU* 3.8 3.4 - - - -
326A ARG* 5.7 1.4 - - - +
334A VAL* 3.7 28.0 - - + -
335A ILE* 1.3 81.7 - - - +
337A GLU* 1.3 64.6 + - - +
359A ALA* 3.4 3.2 - - - +
360A GLY* 2.7 54.1 + - - +
361A GLY* 3.5 7.4 - - - -
380A VAL* 3.4 12.4 - - + +
381A GLY 2.9 17.9 + - - -
382A LEU* 4.3 4.3 - - + -
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Residues in contact with GLU 337 (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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195A MET* 5.0 0.2 - - - -
209A VAL* 4.3 2.9 - - - +
210A LYS* 2.8 41.0 + - + +
242A ASP* 4.4 6.1 - - - +
324A LEU* 3.6 20.2 - - + +
326A ARG* 2.8 51.9 + - - -
336A TYR* 1.3 77.7 - - - +
338A ALA* 1.3 61.4 + - - +
339A VAL* 3.9 8.8 + - + +
356A SER* 3.5 29.7 + - - -
358A ALA 3.3 16.2 - - - +
359A ALA* 4.2 7.1 - - + +
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Residues in contact with ALA 338 (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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195A MET* 4.0 11.0 - - - -
199A LEU* 3.5 32.3 - - + -
207A PHE* 5.2 0.2 - - + -
208A LEU 3.4 5.8 - - - +
209A VAL* 4.1 9.2 - - + +
337A GLU* 1.3 73.0 - - - +
339A VAL* 1.3 58.8 + - - +
356A SER* 3.1 10.7 - - - -
357A VAL* 3.0 26.0 + - + -
358A ALA* 2.8 24.1 + - + +
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Residues in contact with VAL 339 (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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207A PHE* 3.1 6.3 - - - -
208A LEU* 2.7 46.0 + - + +
210A LYS* 4.0 28.9 - - + +
242A ASP* 6.2 0.2 - - - +
337A GLU* 4.3 12.6 - - + +
338A ALA* 1.3 82.7 - - - +
340A LEU* 1.3 76.7 + - - +
341A LEU* 5.1 2.5 - - + -
353A GLY* 3.6 21.3 - - - -
354A VAL 3.9 1.8 - - - +
355A GLY 3.3 12.6 - - - +
356A SER* 4.2 13.2 - - - +
357A VAL* 4.7 0.9 - - - +
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Residues in contact with LEU 340 (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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204A ILE* 3.8 40.8 - - + +
206A ASP 3.5 12.3 - - - +
207A PHE* 4.2 9.9 - - + -
339A VAL* 1.3 78.7 - - - +
341A LEU* 1.3 62.1 + - - +
353A GLY* 3.5 1.4 - - - -
354A VAL* 2.9 42.4 + - + +
355A GLY 2.8 14.4 + - - +
357A VAL* 3.7 21.0 - - + +
388A ARG* 5.0 3.8 - - - -
392A ILE* 3.4 33.0 - - + -
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Residues in contact with LEU 341 (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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206A ASP* 2.8 45.2 + - + +
207A PHE* 3.6 28.3 - - - +
208A LEU* 4.0 20.6 - - + -
317A LYS* 5.8 0.2 - - - +
339A VAL* 4.6 2.5 - - + +
340A LEU* 1.3 83.2 - - - +
342A GLN* 1.3 64.9 + - - +
351A PRO* 4.0 23.8 - - + -
352A LEU 3.5 26.5 - - - +
353A GLY* 4.2 3.4 - - - +
354A VAL* 4.2 6.1 - - - +
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Residues in contact with GLN 342 (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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341A LEU* 1.3 78.9 - - - +
343A THR* 1.3 80.7 + - - +
351A PRO* 4.6 3.1 - - - +
352A LEU* 3.1 49.6 + - + +
353A GLY 5.4 0.3 - - - +
354A VAL* 3.6 22.3 - - + +
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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