Contacts of the helix formed by residues 79 - 88 (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 GLY 79 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU 4.2 0.4 + - - -
78D HIS* 1.3 74.4 - - - +
80D TYR* 1.3 60.8 + - - -
81D GLU* 3.5 2.2 - - - -
82D VAL* 3.1 19.0 - - - +
83D VAL* 3.1 16.4 - - - +
393D SER* 3.0 25.7 + - - -
394D VAL* 4.5 2.5 - - - -
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Residues in contact with TYR 80 (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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79D GLY* 1.3 69.4 - - - -
81D GLU* 1.3 69.8 + - + +
83D VAL* 4.8 0.7 - - - -
84D LYS* 2.8 69.8 + - + +
88D ILE* 5.0 4.5 - - + +
393D SER 5.3 0.6 + - - -
394D VAL* 4.4 26.3 - - + +
423D ASN* 3.4 42.2 + - + +
424D TYR* 3.7 48.5 - + + +
426D MET* 4.5 11.2 - - + -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PRO* 6.0 0.7 - - - +
79D GLY 3.5 0.4 - - - -
80D TYR* 1.3 85.2 - - + +
82D VAL* 1.3 58.9 + - + +
84D LYS* 3.8 4.5 - - - +
85D GLU* 2.9 39.1 + - - +
377D ARG* 3.4 30.7 + - - +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PRO* 3.3 27.4 - - + -
64D VAL* 4.1 7.2 - - + -
77D LEU* 4.2 10.5 - - + -
78D HIS 3.3 32.8 - - - +
79D GLY* 3.1 22.2 - - - +
81D GLU* 1.3 75.1 - - + +
83D VAL* 1.3 66.1 + - - +
85D GLU* 4.5 0.2 - - - -
86D ALA* 3.0 22.0 + - - +
376D PHE* 3.3 33.3 - - + -
377D ARG* 3.9 17.0 - - - +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 3.8 30.1 - - + +
79D GLY 3.1 20.8 + - - +
80D TYR* 4.0 1.8 - - - +
82D VAL* 1.3 75.8 - - - +
84D LYS* 1.3 55.1 + - - +
87D LEU* 2.8 62.0 + - + +
389D THR* 4.4 11.4 - - - -
390D SER 4.4 4.5 - - - +
391D LEU* 5.0 6.1 - - + -
394D VAL* 4.3 15.3 - - + -
426D MET* 4.2 23.1 - - + -
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Residues in contact with LYS 84 (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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80D TYR* 2.8 51.5 + - + +
81D GLU* 3.8 5.4 - - - +
83D VAL* 1.3 74.6 - - - +
85D GLU* 1.3 66.2 + - + +
87D LEU* 5.0 0.2 - - - -
88D ILE* 2.7 67.2 + - + +
89D ASP* 3.3 24.7 + - - +
426D MET* 5.1 2.5 - - - -
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Residues in contact with GLU 85 (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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81D GLU* 2.9 24.3 + - - +
82D VAL 3.8 3.4 - - - +
84D LYS* 1.3 81.1 - - + +
86D ALA* 1.3 57.9 + - - +
89D ASP* 3.0 28.1 - - - +
90D LEU* 2.9 32.1 + - + +
376D PHE* 4.1 15.1 - - + +
377D ARG* 2.8 44.4 + - - +
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Residues in contact with ALA 86 (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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77D LEU* 3.4 16.8 - - + -
82D VAL 3.0 17.1 + - - +
83D VAL 4.0 0.4 - - - +
85D GLU* 1.3 75.5 - - - +
87D LEU* 1.3 60.8 + - + +
90D LEU* 2.7 35.6 - - - +
94D PHE* 3.3 32.5 - - + -
376D PHE* 3.4 20.6 - - + -
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Residues in contact with LEU 87 (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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77D LEU* 4.5 0.2 - - + -
83D VAL* 2.8 47.4 + - + +
84D LYS* 5.0 0.2 - - - -
86D ALA* 1.3 81.4 - - + +
88D ILE* 1.3 61.8 + - + +
91D GLY* 3.4 16.6 - - - +
94D PHE* 4.6 13.7 - - + +
368D HIS* 3.6 31.0 - - + +
389D THR* 3.2 29.6 - - + -
426D MET* 5.5 0.2 - - + -
429D SER* 4.9 4.0 - - - +
430D ALA* 3.4 34.8 - - + +
431D GLY* 3.4 16.4 - - - -
432D LYS 4.5 0.6 + - - +
433D ARG* 5.7 0.7 - - + -
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Residues in contact with ILE 88 (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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80D TYR* 5.0 5.4 - - + +
84D LYS* 2.7 49.7 + - + +
87D LEU* 1.3 72.9 - - + +
89D ASP* 1.3 79.9 + - - +
91D GLY* 3.3 9.9 + - - -
426D MET* 4.9 10.3 - - + -
430D ALA* 4.7 15.5 - - + -
431D GLY* 4.9 4.5 - - - +
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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