Contacts of the helix formed by residues 418 - 426 (chain D) in PDB entry 3GZN
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 VAL 418 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D LEU* 3.5 19.1 - - + +
416D GLN 4.7 0.4 - - - -
417D SER* 1.3 81.5 - - - +
419D THR* 1.3 66.4 + - - +
420D SER* 3.2 5.4 - - - +
421D ILE* 2.9 43.6 + - + +
422D GLU* 3.0 12.5 + - - -
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Residues in contact with THR 419 (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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416D GLN 5.0 1.5 + - - -
417D SER 4.1 2.2 + - - -
418D VAL* 1.3 70.5 - - - +
420D SER* 1.3 60.5 + - - +
422D GLU* 3.7 8.4 - - - +
423D GLU* 3.1 32.2 + - - +
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Residues in contact with SER 420 (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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418D VAL* 3.0 4.8 + - - -
419D THR* 1.3 78.3 - - - +
421D ILE* 1.3 68.1 + - - +
423D GLU* 3.4 10.5 + - - +
424D ARG* 3.3 24.7 + - - +
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Residues in contact with ILE 421 (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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412D THR* 4.3 15.9 - - + -
415D LEU* 3.8 28.9 - - + -
418D VAL* 2.9 31.3 + - + +
420D SER* 1.3 78.0 - - - +
422D GLU* 1.3 66.6 + - - +
424D ARG* 3.4 6.9 + - + +
425D THR* 3.0 31.5 + - + +
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Residues in contact with GLU 422 (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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414D TYR* 3.0 26.5 + - + +
415D LEU 3.3 26.5 + - - +
416D GLN* 4.4 11.9 - - + +
418D VAL 3.0 12.4 + - - +
419D THR* 3.7 12.6 - - - +
421D ILE* 1.3 77.6 - - - +
423D GLU* 1.3 68.6 + - - +
425D THR* 3.5 1.9 + - - -
426D ARG* 3.0 64.7 + - - +
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Residues in contact with GLU 423 (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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419D THR* 3.1 21.2 + - - +
420D SER* 3.6 8.4 - - - +
421D ILE 3.3 0.2 - - - -
422D GLU* 1.3 90.5 + - - +
424D ARG* 1.3 61.9 + - - +
425D THR 3.4 0.5 + - - -
426D ARG* 3.6 17.8 + - - +
427D PRO* 3.9 8.0 - - - +
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Residues in contact with ARG 424 (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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420D SER* 3.3 14.4 + - - +
421D ILE* 3.4 11.6 + - + +
423D GLU* 1.3 79.1 - - + +
425D THR* 1.3 64.7 + - + +
427D PRO* 3.7 13.2 - - - +
428D ASN* 5.6 0.3 - - - +
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Residues in contact with THR 425 (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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412D THR* 3.8 17.7 - - + +
413D LEU 3.3 21.9 - - - +
414D TYR* 3.2 25.6 - - - -
415D LEU 3.7 3.5 + - - -
421D ILE* 3.0 29.6 + - + +
422D GLU* 3.5 1.2 + - - -
424D ARG* 1.3 80.8 - - + +
426D ARG* 1.3 66.1 + - - +
427D PRO* 3.3 4.0 - - - -
428D ASN* 2.9 29.7 + - - +
429D LEU 4.3 0.2 + - - -
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Residues in contact with ARG 426 (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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414D TYR* 3.8 10.8 - - + +
422D GLU* 3.0 54.2 + - - +
423D GLU* 3.9 12.5 - - - +
424D ARG 3.6 0.2 - - - -
425D THR* 1.3 75.7 + - - +
427D PRO* 1.4 72.2 - - + +
429D LEU* 3.1 34.5 + - + +
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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