Contacts of the helix formed by residues 331 - 341 (chain A) in PDB entry 6R4E
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 GLU 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A GLN* 4.7 11.7 + - - -
321A PHE* 4.1 18.7 - - + -
327A LYS* 2.9 53.8 + - + +
328A GLU* 4.1 5.2 + - - +
329A ILE 3.2 0.2 - - - -
330A PHE* 1.3 76.7 - - - +
332A GLN* 1.3 58.9 + - - +
333A PRO* 3.2 4.3 - - - -
334A GLU* 2.9 46.3 + - - +
335A SER* 3.0 14.0 + - - -
476A LYS* 5.7 5.2 + - + -
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Residues in contact with GLN 332 (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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328A GLU 3.5 14.8 + - - +
329A ILE* 2.9 38.3 + - - +
331A GLU* 1.3 78.4 - - - +
333A PRO* 1.3 67.6 - - + +
335A SER* 3.2 11.5 + - - +
336A VAL* 3.0 28.6 + - + +
475A THR* 3.3 13.0 - - - +
476A LYS* 3.9 7.4 - - - -
479A THR* 3.0 42.2 + - - +
517A ILE* 4.3 14.1 - - + -
651A ILE* 4.0 22.1 - - - +
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Residues in contact with PRO 333 (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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330A PHE 3.4 12.8 - - - +
331A GLU 3.2 5.4 - - - -
332A GLN* 1.3 93.4 - - + +
334A GLU* 1.3 60.8 + - + +
336A VAL* 4.2 1.0 - - - +
337A VAL* 3.2 27.5 + - - +
514A PRO* 3.7 27.7 - - + +
517A ILE* 3.6 23.3 - - + -
518A LYS* 3.7 34.3 - - + -
521A LEU* 3.9 8.3 - - + -
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Residues in contact with GLU 334 (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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331A GLU* 2.9 37.3 + - + +
333A PRO* 1.3 80.9 - - + +
335A SER* 1.3 60.7 + - - +
336A VAL 3.3 0.2 - - - -
337A VAL* 3.2 8.5 + - - +
338A ASN* 2.9 38.4 + - - +
518A LYS* 6.3 1.6 - - - -
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Residues in contact with SER 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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331A GLU* 3.0 9.7 + - - -
332A GLN* 3.2 21.2 + - - +
334A GLU* 1.3 74.1 - - - +
336A VAL* 1.3 67.8 + - - +
338A ASN* 3.3 12.2 + - - +
339A THR* 3.0 28.8 + - - -
465A ASN 4.2 1.4 - - - +
466A ALA* 4.0 20.2 - - - +
476A LYS* 3.6 25.0 - - - +
479A THR* 4.7 0.5 + - - -
480A SER* 3.7 7.6 + - - -
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Residues in contact with VAL 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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332A GLN* 3.0 22.6 + - + +
333A PRO 4.2 3.4 - - - +
335A SER* 1.3 79.0 + - - +
337A VAL* 1.3 61.6 + - - +
339A THR* 3.2 16.8 + - - -
340A MET* 3.2 30.5 + - + +
479A THR* 4.5 21.3 - - - +
480A SER* 4.7 1.1 - - - +
483A VAL* 4.2 20.4 - - + -
513A LEU* 4.0 24.9 - - + -
514A PRO* 4.7 7.0 - - + -
517A ILE* 3.8 19.3 - - + -
647A ILE* 5.3 0.4 - - + -
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Residues in contact with VAL 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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333A PRO 3.2 17.4 + - - +
334A GLU* 3.2 10.9 + - - +
336A VAL* 1.3 78.5 - - - +
338A ASN* 1.3 61.1 + - - +
340A MET* 3.1 12.6 + - + +
341A ARG* 3.0 49.6 + - - +
514A PRO* 3.5 25.8 - - + -
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Residues in contact with ASN 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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315A GLN* 5.6 6.5 - - - +
334A GLU* 2.9 28.7 + - - +
335A SER* 3.7 7.3 - - - +
336A VAL 3.3 0.2 - - - -
337A VAL* 1.3 74.9 - - - +
339A THR* 1.3 63.0 + - - +
340A MET 3.3 0.5 + - - -
341A ARG* 3.2 41.4 + - - +
343A ARG* 4.9 0.7 + - - -
465A ASN* 3.1 44.0 + - - +
466A ALA 5.3 4.4 + - - -
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Residues in contact with THR 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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335A SER 3.0 7.9 + - - -
336A VAL* 3.2 12.1 + - - -
338A ASN* 1.3 77.3 - - - +
340A MET* 1.3 57.3 + - - +
341A ARG 3.5 0.2 - - - -
343A ARG* 3.0 31.3 + - - +
464A ILE 2.8 22.1 + - - +
465A ASN 3.8 1.4 + - - -
480A SER* 2.8 36.0 + - - +
483A VAL* 4.1 9.6 - - + -
484A SER* 3.4 26.0 - - - +
487A MET* 3.4 12.4 - - + +
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Residues in contact with MET 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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336A VAL* 3.5 28.5 - - + +
337A VAL* 3.1 15.6 + - + +
339A THR* 1.3 75.6 - - - +
341A ARG* 1.3 67.3 + - - +
342A GLY 3.4 0.2 + - - -
343A ARG* 3.0 14.5 + - - +
344A VAL* 3.2 22.1 + - + +
346A PHE* 4.3 19.1 - - + -
483A VAL* 3.8 26.0 - - + -
487A MET* 4.2 11.7 - - - -
510A LEU* 3.7 46.9 - - - +
511A LYS* 5.5 0.2 - - - -
514A PRO* 4.5 8.1 - - + -
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Residues in contact with ARG 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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337A VAL* 3.0 38.6 + - - +
338A ASN* 3.2 38.7 + - - +
340A MET* 1.3 78.1 - - - +
342A GLY* 1.3 61.6 + - - +
343A ARG* 3.1 16.5 + - - +
465A ASN* 5.4 2.4 + - - +
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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