Contacts of the helix formed by residues 338 - 344 (chain D) in PDB entry 4GQS
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 338 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D GLU* 4.1 4.0 - - - +
146D GLN* 3.1 19.1 - - - +
336D SER 4.6 3.1 - - - +
337D PRO* 1.3 73.4 - - - +
339D MET* 1.3 61.1 + - - +
340D GLN* 3.1 37.0 - - - -
341D ASP* 3.1 31.3 + - - +
446D PHE* 3.3 19.1 - - - -
447D LEU* 3.7 6.1 - - - -
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Residues in contact with MET 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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142D GLU* 3.2 30.2 + - - +
338D CYS* 1.3 71.9 - - - +
340D GLN* 1.3 63.3 + - + +
341D ASP 3.0 4.9 - - - -
342D ARG* 2.9 65.7 + - - +
343D GLY 4.0 1.6 + - - -
439D GLY 5.6 0.2 - - - +
442D ARG 4.6 0.7 - - - +
443D MET* 3.4 52.0 - - + +
446D PHE* 4.1 6.3 - - - -
447D LEU* 4.1 15.9 - - - -
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Residues in contact with GLN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 5.6 4.9 - - - +
93C GLU* 3.5 23.4 + - - +
375C LYS* 6.1 1.4 - - - +
338D CYS* 3.1 16.1 - - - -
339D MET* 1.3 80.5 - - + +
341D ASP* 1.3 60.6 + - - +
342D ARG 3.3 0.2 - - - -
343D GLY* 3.9 7.2 + - - -
344D HIS* 4.1 14.6 + - - -
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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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330D VAL* 4.5 11.1 - - + +
331D VAL* 4.0 30.4 - - + +
335D ARG* 5.6 7.2 + - - -
336D SER 4.5 2.3 - - - +
337D PRO* 4.0 5.2 - - + +
338D CYS* 3.1 38.8 + - - +
339D MET 3.0 0.8 - - - -
340D GLN* 1.3 79.1 - - - +
342D ARG* 1.3 64.6 + - - +
343D GLY 3.3 0.4 - - - -
344D HIS* 3.1 16.2 + - - +
345D MET* 3.2 22.3 - - + +
446D PHE* 4.9 1.3 - - + -
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Residues in contact with ARG 342 (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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375C LYS* 5.9 3.6 - - - +
339D MET* 2.9 41.9 + - - +
341D ASP* 1.3 78.3 - - - +
343D GLY* 1.3 59.7 + - - +
345D MET* 2.8 29.5 + - - +
349D ASP* 3.5 28.2 + - + +
442D ARG* 3.8 38.7 + - - +
446D PHE* 3.3 49.2 - - + -
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Residues in contact with GLY 343 (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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375C LYS* 6.0 3.4 - - - -
339D MET 4.0 2.2 + - - -
340D GLN 3.9 6.9 + - - -
341D ASP 3.3 1.0 - - - -
342D ARG* 1.3 81.7 - - - +
344D HIS* 1.3 64.0 + - - +
345D MET 3.3 2.0 + - - -
346D PRO* 5.1 1.4 - - - +
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Residues in contact with HIS 344 (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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326D GLU* 4.7 0.9 - - - +
329D ARG* 5.1 2.1 + - - -
330D VAL* 3.8 23.3 - - + +
340D GLN 4.1 13.3 + - - -
341D ASP* 3.1 9.6 + - - +
342D ARG 3.1 1.0 - - - -
343D GLY* 1.3 80.2 - - - +
345D MET* 1.3 63.3 + - - +
346D PRO* 3.5 10.3 - - - +
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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