Contacts of the helix formed by residues 382 - 391 (chain A) in PDB entry 6GE3
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A LEU* 3.3 1.1 - - - +
381A PRO* 1.3 100.9 - - + +
383A LYS* 1.3 65.4 + - - +
384A TYR* 3.4 36.5 - - + -
385A MET* 3.1 28.2 + - + +
386A MET* 3.3 15.8 + - - +
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Residues in contact with LYS 383 (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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382A GLU* 1.3 73.2 + - - +
384A TYR* 1.3 62.4 + - - +
386A MET* 3.1 17.1 + - + +
387A ASN* 3.1 37.9 + - - +
417A VAL* 4.0 34.7 + - + +
418A SER 4.6 7.0 - - - +
419A ALA* 4.2 20.8 - - + +
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Residues in contact with TYR 384 (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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382A GLU* 3.3 38.9 - - + -
383A LYS* 1.3 79.5 - - - +
385A MET* 1.3 83.9 + - + +
387A ASN* 3.5 10.2 + - - +
388A SER* 3.0 38.3 + - - -
72L VAL* 5.8 1.8 - - + -
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Residues in contact with MET 385 (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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380A LEU* 3.9 16.8 - - + -
381A PRO* 3.8 30.3 - - + -
382A GLU* 3.1 19.4 + - + +
384A TYR* 1.3 111.7 - - + +
386A MET* 1.3 63.2 + - - +
388A SER* 3.2 4.1 + - - -
389A VAL* 3.0 27.0 + - - +
72L VAL* 3.6 38.6 - - + +
73L MET* 4.7 12.6 - - - +
75L PRO* 6.3 0.2 - - + -
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Residues in contact with MET 386 (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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302A LEU* 4.0 23.1 - - + -
377A LEU* 3.4 35.8 - - + +
378A LYS* 4.2 10.8 - - + +
380A LEU* 3.6 30.7 - - + +
381A PRO 5.4 0.2 - - - -
382A GLU 3.7 15.7 - - - +
383A LYS* 3.1 14.9 + - + +
385A MET* 1.3 76.5 - - - +
387A ASN* 1.3 57.5 + - - +
389A VAL* 3.3 4.0 + - - +
390A LEU* 3.0 33.5 + - - +
417A VAL* 3.7 21.3 - - + -
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Residues in contact with ASN 387 (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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383A LYS* 3.1 38.2 + - - +
384A TYR* 3.9 9.8 - - - +
386A MET* 1.3 72.9 - - - +
388A SER* 1.3 66.1 + - - +
390A LEU* 3.3 5.4 + - - +
391A GLU* 3.0 26.9 + - - +
415A PHE 5.2 0.5 - - - +
416A GLU* 3.4 30.4 + - + +
417A VAL* 2.7 37.1 + - - +
87L ARG* 6.3 0.4 - - - +
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Residues in contact with SER 388 (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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384A TYR* 3.0 29.7 + - - -
385A MET 3.2 10.3 + - - -
387A ASN* 1.3 75.9 - - - +
389A VAL* 1.3 62.3 + - - +
391A GLU* 3.3 24.7 + - - +
392A ASN* 4.4 5.9 + - - -
72L VAL* 4.0 21.7 - - - +
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Residues in contact with VAL 389 (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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373A PHE* 3.6 30.7 - - + -
377A LEU* 4.0 4.9 - - + -
380A LEU* 3.9 17.5 - - + -
385A MET 3.0 17.6 + - - +
386A MET 3.6 7.2 - - - +
388A SER* 1.3 76.3 - - - +
390A LEU* 1.3 62.3 + - - +
392A ASN* 3.2 16.8 + - - +
393A PHE* 3.8 6.1 + - - +
68L LEU* 4.0 24.1 - - + +
69L PHE* 3.8 23.8 - - + -
72L VAL* 3.7 20.9 - - + -
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Residues in contact with LEU 390 (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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300A ALA* 5.9 0.2 - - + -
373A PHE* 3.7 23.3 - - + -
377A LEU* 3.8 7.9 - - + -
386A MET 3.0 20.2 + - - +
387A ASN* 3.3 7.1 + - - +
389A VAL* 1.3 70.7 - - - +
391A GLU* 1.3 65.5 + - - +
392A ASN 3.1 2.9 + - - -
393A PHE* 3.3 30.9 + - + +
394A THR* 5.6 0.2 - - - +
414A VAL* 5.4 2.9 - - - +
415A PHE* 3.4 30.0 + - + +
416A GLU* 3.9 19.7 - - - -
417A VAL* 3.9 25.6 - - + -
501A MYR 3.7 29.8 - - + -
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Residues in contact with GLU 391 (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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273A LYS* 2.9 33.7 + - - +
387A ASN* 3.0 20.5 + - - +
388A SER* 3.3 17.5 - - - +
389A VAL 3.2 0.4 - - - -
390A LEU* 1.3 77.4 - - - +
392A ASN* 1.3 68.4 + - - +
393A PHE 3.9 1.0 + - - +
394A THR* 5.1 0.5 - - - +
414A VAL* 6.0 1.8 - - - +
415A PHE 5.4 0.4 - - - -
416A GLU* 5.7 2.1 - - - +
83L THR* 5.2 4.9 - - + +
84L VAL 4.4 1.7 - - - +
85L PRO* 3.5 13.0 - - - +
86L MET* 3.0 47.9 + - - +
87L ARG* 5.0 7.8 + - - +
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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