Contacts of the helix formed by residues 75 - 86 (chain D) in PDB entry 4XQ2
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 SER 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ARG* 4.4 7.0 - - - -
229C GLY* 2.7 32.3 + - - -
231C VAL* 4.7 5.4 - - - -
73D PHE* 3.1 9.2 - - - +
74D SER* 1.3 80.8 - - - +
76D GLY* 1.3 65.7 + - - +
77D GLN 3.6 1.7 + - - -
78D ALA* 3.2 15.2 + - - +
79D ALA* 3.1 18.5 + - - +
196D THR* 5.1 3.1 - - - -
197D LLP 3.4 15.8 + - - -
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Residues in contact with GLY 76 (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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75D SER* 1.3 68.0 - - - +
77D GLN* 1.3 66.1 + - - +
79D ALA* 3.0 6.2 + - - +
80D ALA* 2.8 23.5 + - - +
192D LEU* 4.4 2.8 - - - +
193D TYR 3.9 20.2 - - - -
194D SER* 4.0 6.0 - - - +
195D THR 5.3 1.2 - - - +
197D LLP 2.8 34.8 + - - -
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Residues in contact with GLN 77 (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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48C ARG* 3.4 33.0 - - - +
226C THR 4.0 0.2 - - - +
227C THR* 2.5 38.0 + - - +
228C ALA 3.4 2.2 - - - -
229C GLY* 3.8 8.3 - - - -
75D SER* 3.4 5.6 - - - +
76D GLY* 1.3 69.9 - - - +
78D ALA* 1.3 51.6 + - - +
80D ALA* 3.2 3.0 + - - +
81D ALA* 2.6 37.8 + - - +
100D TYR* 3.3 13.0 - - - -
102D GLY* 2.8 49.1 + - - -
103D THR* 3.6 2.9 + - - -
106D LEU* 3.3 12.7 - - - +
197D LLP 2.9 16.4 + - - +
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Residues in contact with ALA 78 (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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228C ALA 3.0 18.7 + - - +
229C GLY 3.6 9.2 - - - +
230C ASN* 4.8 2.7 - - + +
73D PHE* 3.9 17.7 - - + -
74D SER* 4.4 4.5 - - - +
75D SER* 3.2 20.2 + - - +
76D GLY 3.1 0.8 - - - -
77D GLN* 1.3 72.6 - - - +
79D ALA* 1.3 65.5 + - - +
81D ALA* 3.8 2.9 - - - +
82D THR* 2.9 30.4 + - - -
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Residues in contact with ALA 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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73D PHE* 3.7 30.2 - - + +
75D SER 3.1 9.9 + - - +
76D GLY 3.0 10.2 + - - +
78D ALA* 1.3 74.1 - - - +
80D ALA* 1.3 64.0 + - - +
82D THR* 3.3 4.2 + - - -
83D LEU* 3.2 22.0 + - - +
192D LEU* 3.7 17.5 - - + +
193D TYR 4.3 11.4 - - - +
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Residues in contact with ALA 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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76D GLY 2.8 12.2 + - - +
77D GLN* 3.5 10.5 - - - +
79D ALA* 1.3 74.7 - - - +
81D ALA* 1.3 65.4 + - - +
82D THR 3.3 0.2 + - - -
83D LEU* 3.4 3.4 + - - +
84D LEU* 3.1 27.8 + - + +
103D THR* 5.0 5.8 - - + +
106D LEU* 3.6 15.3 - - + -
141D TRP* 3.6 25.3 - - + -
192D LEU* 3.4 16.0 - - + +
197D LLP 6.2 1.6 - - + -
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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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228C ALA* 4.0 16.8 - - + +
77D GLN 2.6 20.7 + - - +
78D ALA* 3.8 4.9 - - - +
79D ALA 3.3 0.2 - - - -
80D ALA* 1.3 72.5 - - - +
82D THR* 1.3 62.7 + - - +
84D LEU* 3.4 5.3 + - - +
85D SER* 3.1 23.4 + - - -
106D LEU* 3.4 26.6 - - + +
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Residues in contact with THR 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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73D PHE* 3.1 34.9 - - + -
78D ALA* 2.9 22.4 + - - +
79D ALA 3.5 4.9 - - - -
80D ALA 3.2 0.2 - - - -
81D ALA* 1.3 74.6 - - - +
83D LEU* 1.3 68.6 + - - +
85D SER* 2.7 27.4 + - - +
86D LEU* 3.9 10.2 - - + +
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Residues in contact with LEU 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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79D ALA 3.2 11.0 + - - +
80D ALA* 3.9 7.6 - - - +
82D THR* 1.3 81.4 - - - +
84D LEU* 1.3 60.9 + - - +
86D LEU* 3.5 23.8 + - + +
87D VAL* 4.4 4.3 + - - +
139D LEU* 4.1 13.7 - - + +
141D TRP* 4.2 10.3 - - + -
168D ARG* 4.3 19.9 + - - +
170D VAL* 3.5 46.7 - - + -
190D VAL* 4.2 27.6 - - + -
192D LEU* 5.3 4.7 - - + -
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Residues in contact with LEU 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 ALA 3.1 26.5 + - - +
81D ALA* 3.8 5.4 - - - +
83D LEU* 1.3 74.5 - - - +
85D SER* 1.3 64.3 + - - +
86D LEU 3.0 2.7 - - - -
87D VAL* 3.0 28.3 + - + +
93D VAL* 4.6 11.7 - - + -
103D THR* 5.0 1.1 - - + +
106D LEU* 3.7 33.7 - - + +
107D PHE* 3.5 34.5 - - + -
110D ALA* 5.1 16.1 - - + +
115D VAL* 5.4 1.7 - - - +
139D LEU* 4.3 9.4 - - + -
141D TRP* 3.7 22.2 - - + -
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Residues in contact with SER 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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109C LEU* 6.5 2.5 - - - -
113C GLN* 5.5 2.6 + - - +
81D ALA 3.1 12.1 + - - -
82D THR* 2.7 23.7 + - - +
84D LEU* 1.3 76.8 - - - +
86D LEU* 1.3 67.0 + - - +
87D VAL 3.2 8.4 + - - +
88D ARG* 4.8 9.4 + - - -
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Residues in contact with LEU 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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82D THR* 3.9 13.2 - - + +
83D LEU* 3.6 22.7 - - + +
84D LEU 3.0 1.0 - - - -
85D SER* 1.3 81.3 - - - +
87D VAL* 1.3 62.8 + - + +
88D ARG* 3.6 13.4 + - - +
91D GLN* 4.6 0.5 - - - +
168D ARG* 3.8 30.7 + - - +
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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