Contacts of the strand formed by residues 336 - 343 (chain A) in PDB entry 4GHI
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 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 4.0 15.0 - - + -
248A HIS 3.3 15.0 - - - +
249A SER* 4.7 0.9 - - - +
250A MET* 3.9 8.0 - - - -
325A VAL* 3.6 5.9 - - - +
326A ILE* 2.8 50.5 + - - +
335A GLN* 1.3 83.2 - - - +
337A ILE* 1.3 65.9 + - - +
338A MET* 5.2 0.9 - - - -
362B ARG* 3.8 40.2 - - - +
460B THR* 4.8 2.5 - - - -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 3.2 8.5 - - - +
248A HIS* 2.8 39.0 + - + +
249A SER 3.9 15.0 - - - +
250A MET* 3.9 34.1 - - + +
252A MET* 5.1 2.0 - - + -
293A HIS* 4.3 8.7 - - + +
296A LEU* 3.7 23.6 - - + -
297A CYS* 5.1 0.2 - - - -
324A THR 3.5 7.2 - - - +
325A VAL* 4.4 4.7 - - + -
336A CYS* 1.3 77.5 - - - +
338A MET* 1.3 66.1 + - - +
339A CYS* 3.8 17.6 + - - -
401A 0X3 3.5 30.1 - - - +
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Residues in contact with MET 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.6 26.2 - - + -
246A SER 3.6 7.4 - - - +
247A GLU* 4.9 4.0 - - + -
322A GLN 3.7 0.9 - - - +
323A GLY* 3.4 2.8 - - - -
324A THR* 2.8 38.7 + - - +
326A ILE* 4.3 14.1 - - + +
336A CYS* 4.2 0.6 - - - -
337A ILE* 1.3 72.5 - - - +
339A CYS* 1.3 82.4 + - - +
340A VAL* 5.1 0.4 - - + -
364B ILE* 3.3 37.9 - - + -
444B PHE* 3.8 31.3 - - + -
458B ILE* 3.9 19.5 - - + -
460B THR* 4.2 10.1 - - - +
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Residues in contact with CYS 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.4 6.2 - - - -
246A SER* 2.8 49.7 + - - +
248A HIS* 3.8 6.3 - - - -
321A THR* 3.7 11.7 - - + -
322A GLN 3.4 2.9 - - - -
323A GLY* 4.3 3.1 - - - -
337A ILE* 3.8 15.3 - - - -
338A MET* 1.3 80.1 - - - +
340A VAL* 1.3 63.6 + - - +
341A ASN* 3.6 12.7 + - - +
401A 0X3 3.3 42.0 - - - -
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.7 16.4 - - + -
244A PHE 4.1 1.8 - - - -
245A LEU* 4.0 19.3 - - + -
321A THR* 3.4 1.7 - - - -
322A GLN* 2.9 40.2 + - + +
339A CYS* 1.3 74.5 - - - +
341A ASN* 1.3 62.8 + - - +
342A TYR* 3.9 4.5 - - - -
444B PHE* 4.1 27.8 - - + -
446B PHE* 3.7 50.5 - - + -
456B TYR* 4.6 1.8 - - + +
458B ILE* 4.3 8.5 - - + -
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Residues in contact with ASN 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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242A LYS 3.9 0.3 - - - +
243A THR* 3.2 6.9 - - - +
244A PHE* 3.0 70.6 + - + +
246A SER* 3.0 30.7 + - - +
319A LEU* 4.8 5.2 - - + -
320A GLU 3.6 4.7 - - - -
321A THR* 2.6 36.4 + - - +
339A CYS* 3.6 3.5 + - - +
340A VAL* 1.3 73.8 - - - +
342A TYR* 1.3 61.6 + - - +
401A 0X3 3.2 22.4 - - - -
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Residues in contact with TYR 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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242A LYS* 3.4 8.5 - - + +
243A THR* 4.2 7.0 - - + +
303A VAL* 4.3 5.5 - - - +
319A LEU* 3.5 2.8 - - - +
320A GLU* 2.3 93.8 + - + +
321A THR 5.0 0.5 - - - -
322A GLN* 4.3 7.6 + - + +
340A VAL* 3.9 10.1 - - + -
341A ASN* 1.3 77.7 - - - +
343A VAL* 1.3 66.8 + - - +
344A LEU* 3.7 11.3 + - + +
446B PHE* 3.8 28.2 - + - -
448B ASN* 3.9 27.1 - - - +
449B PRO* 3.8 25.7 - - + +
450B TYR* 4.4 8.3 - + - -
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Residues in contact with VAL 343 (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 LYS* 2.9 45.1 + - + +
244A PHE* 4.4 6.1 - - + -
264A LEU* 3.8 38.4 - - + +
265A ILE* 4.7 1.1 - - + -
317A VAL* 3.3 16.6 - - + -
318A TRP 3.6 3.6 - - - -
319A LEU* 3.3 19.1 - - + -
342A TYR* 1.3 74.9 - - - +
344A LEU* 1.3 63.1 + - - +
345A SER 2.9 29.8 - - - +
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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