Contacts of the helix formed by residues 78 - 88 (chain D) in PDB entry 4K9N
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 ALA 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D GLU 3.8 8.1 - - - +
48D ALA* 4.2 8.3 - - - +
51D VAL* 3.6 28.0 - - + -
69D LEU* 3.8 16.8 - - + -
74D GLY 3.3 2.8 + - - +
75D THR 2.9 11.4 + - - +
77D ASN* 1.3 78.7 - - - +
79D MET* 1.3 62.3 + - - +
80D GLY 3.3 3.1 - - - -
81D ALA* 3.2 8.1 + - - +
82D LEU* 3.0 25.0 + - + +
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Residues in contact with MET 79 (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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76B GLY* 3.4 23.1 - - - +
79B MET* 4.2 9.4 - - + -
118B LEU* 3.7 17.3 - - + +
75D THR* 3.5 17.7 - - + +
76D GLY* 3.1 15.3 + - - +
77D ASN 3.4 0.2 - - - -
78D ALA* 1.3 79.8 - - - +
80D GLY* 1.3 60.9 + - - +
82D LEU* 3.4 20.3 + - - -
83D SER* 3.2 15.4 + - - -
118D LEU* 3.7 8.5 - - + +
119D PRO* 3.3 46.2 - - + +
122D LEU* 3.3 31.4 - - + +
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Residues in contact with GLY 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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73B ALA* 3.6 22.0 - - - +
76B GLY* 3.3 9.9 - - - -
77B ASN* 3.3 19.7 + - - +
78D ALA 3.3 0.6 - - - -
79D MET* 1.3 73.5 - - - +
81D ALA* 1.3 65.1 + - - +
83D SER* 3.0 23.0 + - - -
84D ASN* 3.5 10.4 + - - -
402D GLY* 5.5 0.2 - - - -
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Residues in contact with ALA 81 (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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77B ASN* 4.2 3.6 + - - -
48D ALA* 4.0 21.8 - - + +
51D VAL* 3.6 28.6 - - + +
52D GLY* 4.3 5.4 - - - +
55D ASP* 4.4 3.5 - - - +
78D ALA* 3.2 11.5 + - - +
80D GLY* 1.3 74.8 - - - +
82D LEU* 1.3 62.6 + - - +
84D ASN* 3.3 14.0 + - - +
85D ALA* 3.1 20.3 + - - +
404D GLY 6.1 0.4 - - - +
405D PHE* 6.6 0.2 - - - -
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Residues in contact with LEU 82 (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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51D VAL* 4.2 16.2 - - + -
69D LEU* 6.3 0.2 - - + -
75D THR* 5.3 4.3 - - + +
78D ALA* 3.0 21.4 + - + +
79D MET* 3.6 31.6 - - - +
80D GLY 3.1 0.6 - - - -
81D ALA* 1.3 73.2 - - - +
83D SER* 1.3 66.5 + - - +
85D ALA* 3.7 2.0 - - - +
86D TRP* 2.9 24.8 + - - +
92D LEU* 4.4 4.3 - - + -
94D VAL* 4.1 27.6 - - + -
119D PRO* 4.5 4.9 - - + -
122D LEU* 4.1 16.8 - - + +
123D VAL* 4.5 16.2 - - + -
153D PRO* 4.0 26.0 - - + +
155D TYR* 5.8 0.9 - - + -
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Residues in contact with SER 83 (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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72B ALA* 4.3 8.8 - - - +
73B ALA* 4.2 24.7 + - - +
79D MET 3.2 11.0 + - - -
80D GLY 3.0 14.2 + - - -
82D LEU* 1.3 77.7 - - - +
84D ASN* 1.3 61.5 + - - +
86D TRP* 3.5 4.5 + - - +
87D ASN* 3.4 15.8 + - - +
122D LEU* 3.7 21.2 - - - +
400D ALA* 3.3 23.1 - - - +
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Residues in contact with ASN 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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55D ASP* 4.5 1.1 - - - +
80D GLY 3.5 7.9 + - - -
81D ALA* 3.3 12.2 + - - +
82D LEU 3.2 0.2 - - - -
83D SER* 1.3 81.2 - - - +
85D ALA* 1.3 62.4 + - - +
87D ASN 3.1 2.6 + - - -
88D SER* 3.0 22.4 + - - -
398D CYS* 3.5 9.1 - - - +
399D ALA* 3.5 11.3 - - + +
400D ALA* 2.9 26.7 + - - +
402D GLY* 2.8 44.6 + - - -
403D LEU 5.1 0.6 + - - -
404D GLY 5.5 0.2 - - - -
405D PHE* 3.6 28.5 - - + +
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Residues in contact with ALA 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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55D ASP* 3.7 10.5 + - - +
81D ALA 3.1 15.7 + - - +
82D LEU* 3.2 8.5 + - + +
84D ASN* 1.3 72.9 - - - +
86D TRP* 1.3 66.5 + - - +
88D SER* 3.3 8.7 + - - -
89D HIS* 3.1 3.8 + - - -
90D SER* 3.0 30.7 + - - -
92D LEU* 3.6 30.5 - - + -
153D PRO* 3.8 12.1 - - + +
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Residues in contact with TRP 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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107B GLU* 5.5 4.8 + - - -
113B VAL* 5.9 6.5 - - + +
82D LEU 2.9 16.5 + - - +
83D SER 3.6 5.6 - - - +
84D ASN 3.2 0.2 - - - -
85D ALA* 1.3 76.2 - - - +
87D ASN* 1.3 77.0 + - - +
89D HIS* 3.3 22.2 + + - -
121D PRO 4.4 11.2 - - - -
122D LEU* 3.4 37.2 - - + +
123D VAL* 3.5 30.3 - - - -
124D LYS* 3.6 17.7 - - + -
151D GLN 5.1 0.2 - - - +
152D GLY* 5.7 0.4 - - - -
153D PRO* 4.0 12.8 - - + +
301D ASP* 5.8 2.5 - - - -
303D LEU* 4.0 26.7 - - + -
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Residues in contact with ASN 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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109B LEU* 4.5 3.2 - - - +
110B LEU 6.0 0.4 - - - +
83D SER 3.4 3.5 + - - +
84D ASN 3.1 3.6 + - - +
86D TRP* 1.3 97.1 - - - +
88D SER* 1.3 58.5 + - - +
89D HIS* 3.3 9.4 + - - -
209D PRO* 5.2 4.5 - - - +
238D PRO* 5.0 4.5 - - - +
279D ARG* 3.6 45.3 + - - +
399D ALA* 3.0 38.9 + - + +
400D ALA* 3.5 19.0 - - - +
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Residues in contact with SER 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ASP* 4.4 0.5 + - - -
59D GLN* 3.6 23.6 + - - +
84D ASN 3.0 12.0 + - - -
85D ALA* 3.3 6.1 + - - -
87D ASN* 1.3 76.2 - - - +
89D HIS* 1.3 71.4 + - - +
90D SER* 2.6 27.7 + - - -
209D PRO* 5.7 5.8 - - - +
210D ASP* 4.5 3.5 - - - +
213D ALA* 5.6 5.4 - - - +
238D PRO* 4.8 7.9 - - - -
239D ARG* 5.6 5.5 + - - -
399D ALA* 3.6 18.8 - - - -
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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