Contacts of the strand formed by residues 334 - 341 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TRP 3.4 2.9 - - - +
242A PHE* 3.8 1.9 - - - -
243A THR* 2.5 42.3 + - + +
245A PRO* 3.5 35.1 - - - +
248A SER* 3.6 20.6 - - - +
305A ASN* 4.1 3.4 - - - +
307A GLY* 3.6 25.8 - - - -
308A ASP* 4.2 6.3 - - - -
333A PRO* 1.3 73.8 - - - +
335A VAL* 1.3 60.8 + - - +
336A LEU 3.6 1.5 + - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 5.0 1.1 - - + -
190A LEU* 4.0 20.6 - - + -
240A VAL* 3.6 26.0 - - + -
241A TRP 3.8 2.9 - - - -
242A PHE* 4.3 8.5 - - + -
305A ASN* 4.8 1.3 - - - -
306A LEU* 3.0 49.4 + - + +
307A GLY 2.8 21.1 + - - +
310A GLU* 5.4 1.1 - - + +
311A LEU* 3.8 36.1 - - + +
334A CYS* 1.3 70.5 - - - +
336A LEU* 1.3 63.4 + - - +
337A SER* 5.0 0.7 - - - -
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Residues in contact with LEU 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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240A VAL* 3.6 6.9 - - - +
241A TRP* 3.0 46.5 + - + +
243A THR* 4.2 10.5 - - + -
248A SER 3.9 7.4 - - - +
251A TRP* 3.6 18.2 - - + -
252A LEU* 3.3 56.8 - - + +
255A TRP* 4.2 8.7 - - + -
304A TRP 3.3 8.5 - - - +
305A ASN* 4.4 9.8 + - - +
334A CYS 3.6 1.8 + - - -
335A VAL* 1.3 74.6 - - - +
337A SER* 1.3 71.2 + - - +
338A VAL* 4.3 20.4 - - + -
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.4 35.7 - - - +
238A SER* 5.0 0.7 + - - -
239A LEU 3.8 2.9 - - - -
240A VAL* 4.6 6.4 - - - +
302A THR 3.7 1.4 - - - +
303A LEU* 3.4 4.9 - - - -
304A TRP* 2.8 41.1 + - - +
306A LEU* 4.4 10.1 - - - -
335A VAL* 5.0 0.4 - - - -
336A LEU* 1.3 78.8 - - - +
338A VAL* 1.3 68.4 + - - +
339A ASN* 4.7 7.6 + - - +
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Residues in contact with VAL 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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114A TRP* 5.6 4.0 - - + +
237A ALA 4.4 0.9 - - - +
238A SER* 3.4 8.3 + - - -
239A LEU* 2.9 53.7 + - + +
241A TRP* 6.1 1.1 - - + -
255A TRP* 4.2 19.5 - - + -
259A ARG* 3.8 22.0 - - + -
301A GLU* 3.4 24.2 - - + +
302A THR 3.8 2.2 - - - -
303A LEU* 4.0 20.9 - - + +
336A LEU* 4.3 9.2 - - + -
337A SER* 1.3 74.5 + - - +
339A ASN* 1.3 65.8 + - - +
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Residues in contact with ASN 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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184A ASN* 4.8 8.5 - - - +
185A LEU* 4.7 11.3 - - - +
186A LEU* 5.2 4.6 - - - +
236A GLU* 3.2 39.2 - - - +
237A ALA 3.5 5.7 - - - +
238A SER* 3.8 20.6 + - - -
300A ILE 4.1 0.2 - - - +
301A GLU* 3.1 5.8 - - - -
302A THR* 2.8 53.0 + - - +
337A SER* 4.7 9.0 + - - +
338A VAL* 1.3 74.4 + - - +
340A GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 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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114A TRP* 6.4 0.2 - - - -
236A GLU* 3.3 10.0 - - - +
237A ALA* 3.0 38.0 + - - +
259A ARG* 5.8 0.2 - - - -
263A TRP* 5.0 4.3 - - - -
300A ILE 3.3 7.9 - - - -
301A GLU* 3.7 18.1 + - - -
339A ASN* 1.3 76.9 + - - +
341A ASP* 1.3 60.8 + - - -
342A LEU* 3.5 2.8 + - - -
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Residues in contact with ASP 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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234A LYS* 3.1 50.5 + - - +
235A THR 4.2 1.1 - - - +
236A GLU* 4.2 12.0 - - - +
263A TRP* 4.0 6.3 - - - -
299A LEU 5.2 0.4 - - - +
300A ILE* 2.6 23.6 + - - +
340A GLY* 1.3 70.3 - - - -
342A LEU* 1.3 60.9 + - - +
343A ASP* 4.5 2.2 + - - +
344A ARG* 3.0 36.6 + - + +
345A GLY* 2.9 23.0 + - - -
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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