Contacts of the strand formed by residues 334 - 341 (chain D) in PDB entry 2G4C
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 CYS 334 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241D TRP 3.1 17.2 - - - +
242D PHE* 3.5 1.6 - - - -
243D THR* 2.6 28.8 + - - +
245D PRO* 4.4 16.2 - - + -
248D SER* 3.4 32.3 - - - +
305D ASN* 4.0 2.2 - - - +
307D GLY* 3.2 29.8 - - - -
308D ASP* 3.7 6.5 - - - -
333D PRO* 1.3 73.8 - - - +
335D VAL* 1.3 62.7 + - - +
336D LEU* 3.3 2.3 + - + +
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Residues in contact with VAL 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D LEU* 5.6 1.6 - - + -
190D LEU* 3.5 17.7 - - + -
240D VAL* 5.0 4.0 - - + -
241D TRP 3.9 2.9 - - - -
242D PHE* 3.4 33.7 - - + -
305D ASN* 3.7 0.7 - - - -
306D LEU* 2.9 56.5 + - + +
307D GLY 2.9 26.2 + - - +
310D GLU* 3.8 12.1 - - + -
311D LEU* 4.1 17.7 - - + +
333D PRO 5.5 0.4 - - - +
334D CYS* 1.3 70.2 - - - +
336D LEU* 1.3 61.7 + - - +
337D SER 3.7 0.9 - - - +
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LEU 3.6 2.1 - - - +
240D VAL* 4.7 1.1 - - - +
241D TRP* 3.0 47.7 + - + +
243D THR* 5.2 4.5 - - + +
248D SER* 4.1 6.7 - - - +
251D TRP* 3.6 16.6 - - + -
252D LEU* 3.1 54.1 - - + +
255D TRP* 4.0 12.8 - - + -
304D TRP 3.1 10.8 - - - +
305D ASN* 4.5 6.5 - - - +
334D CYS* 3.3 3.3 + - + +
335D VAL* 1.3 71.8 - - - +
337D SER* 1.3 60.1 + - - +
338D VAL* 3.9 22.2 - - + -
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Residues in contact with SER 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LEU* 3.1 39.8 - - - +
238D SER* 5.7 1.0 - - - -
239D LEU 3.6 4.2 + - - -
240D VAL* 4.6 1.2 - - - +
302D THR 3.7 2.1 - - - +
303D LEU* 3.4 1.7 - - - -
304D TRP* 2.8 42.8 + - - +
306D LEU* 4.3 14.6 - - - -
335D VAL 3.7 1.6 + - - -
336D LEU* 1.3 73.0 - - - +
338D VAL* 1.3 68.0 + - - +
339D ASN* 4.9 5.7 + - - +
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Residues in contact with VAL 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TRP* 6.3 2.2 - - + -
238D SER* 3.3 5.8 - - - -
239D LEU* 2.7 55.6 + - + +
255D TRP* 4.5 10.3 - - + -
259D ARG* 4.0 13.5 - - - +
301D GLU* 3.4 25.8 - - - +
302D THR 3.7 2.2 - - - +
303D LEU* 3.7 24.0 - - + +
336D LEU* 3.9 20.6 - - + -
337D SER* 1.3 78.6 + - - +
339D ASN* 1.3 67.3 + - - +
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Residues in contact with ASN 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASN* 4.9 5.1 - - - +
185D LEU* 4.7 10.9 - - - +
186D LEU* 5.5 2.4 - - - +
236D GLU* 3.6 34.4 + - - +
237D ALA 3.7 5.6 - - - -
238D SER* 3.7 18.6 - - - -
301D GLU* 3.3 5.6 - - - -
302D THR* 2.9 42.3 + - - +
337D SER* 4.9 6.6 + - - +
338D VAL* 1.3 77.7 - - - +
340D GLY* 1.3 69.6 + - - +
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Residues in contact with GLY 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TRP* 5.8 2.6 - - - +
236D GLU* 3.6 2.4 - - - -
237D ALA* 3.1 35.3 + - - +
259D ARG* 5.7 0.4 - - - -
263D TRP* 4.9 2.9 - - - -
300D ILE 3.5 8.3 - - - -
301D GLU* 3.6 20.1 - - - +
338D VAL* 5.3 0.6 - - - +
339D ASN* 1.3 82.1 - - - +
341D ASP* 1.3 59.4 + - - -
342D LEU* 3.6 2.9 + - - -
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Residues in contact with ASP 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D LYS* 2.7 53.6 + - - +
235D THR 4.1 6.7 - - - +
236D GLU* 4.7 9.3 - - + +
263D TRP* 4.2 5.7 - - - -
299D LEU* 5.2 2.0 - - + +
300D ILE* 2.7 22.6 + - - +
340D GLY* 1.3 68.5 - - - -
342D LEU* 1.3 63.7 + - - +
343D ASP* 3.2 7.1 + - - +
344D ARG* 3.2 22.3 + - + +
345D GLY* 3.0 18.9 + - - -
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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