Contacts of the helix formed by residues 95 - 107 (chain D) in PDB entry 6QPA
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 ASN 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D THR* 3.4 29.9 - - + +
38D SER* 3.5 21.9 + - - -
39D HIS* 5.8 0.2 - - - +
91D MET* 3.0 32.2 + - - +
92D HIS 3.6 2.5 - - - -
94D ASP* 1.3 88.1 + - - +
96D PHE* 1.3 59.1 + - - +
97D LYS 3.3 2.5 - - - -
98D GLU* 3.2 18.3 + - + +
99D ILE* 2.8 32.7 + - + +
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Residues in contact with PHE 96 (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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92D HIS* 3.1 17.6 + - - +
93D HIS 3.3 12.8 + - - +
94D ASP 3.5 1.4 + - - -
95D ASN* 1.3 78.3 - - - +
97D LYS* 1.3 68.4 + - + +
99D ILE* 4.2 4.2 - - + +
100D PHE* 3.0 35.3 + + + +
207D ILE* 3.9 29.8 - - + -
210D PHE* 6.1 3.8 - + - -
212D LEU* 4.5 17.0 - - + -
228D PRO* 4.9 3.6 - - + -
229D PRO* 3.2 43.7 - - + -
230D GLU 4.1 1.3 - - - -
231D TYR* 3.9 39.7 - + + -
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Residues in contact with LYS 97 (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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95D ASN 3.3 0.4 - - - -
96D PHE* 1.3 82.7 - - + +
98D GLU* 1.3 77.6 + - - +
100D PHE* 3.4 2.9 + - - +
101D GLU* 3.0 25.8 + - - +
225D GLY 4.6 2.6 - - - +
228D PRO* 3.9 31.3 - - + +
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Residues in contact with GLU 98 (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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35D THR* 4.4 11.9 - - + +
94D ASP 3.8 6.4 - - - +
95D ASN* 3.3 45.5 - - + +
97D LYS* 1.3 97.5 + - - +
99D ILE* 1.3 64.4 + - - +
101D GLU* 3.2 13.5 + - - +
102D LEU* 3.0 32.5 + - + +
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Residues in contact with ILE 99 (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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32D VAL* 5.5 11.9 - - + +
35D THR* 3.7 17.9 - - + -
36D THR* 5.4 1.8 - - - +
91D MET* 3.8 27.6 - - + -
92D HIS* 3.7 41.3 - - + +
95D ASN* 2.8 29.9 + - + +
96D PHE* 4.2 5.4 - - + +
98D GLU* 1.3 71.6 - - - +
100D PHE* 1.3 58.0 - - - +
102D LEU* 3.3 7.8 + - + +
103D CSS 2.9 44.6 + - + +
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Residues in contact with PHE 100 (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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96D PHE* 3.0 31.7 + + + +
97D LYS 3.6 3.6 - - - +
99D ILE* 1.3 78.6 - - - +
101D GLU* 1.3 57.9 + - - +
103D CSS 4.6 3.4 - - + -
104D SER* 2.8 52.8 + - - -
107D LEU* 6.1 0.4 - - + -
210D PHE* 3.5 38.8 - + - -
220D ALA* 3.5 25.6 - - + -
223D THR* 3.6 21.8 - - + -
225D GLY* 3.8 12.8 - - - -
228D PRO* 3.6 27.1 - - + -
229D PRO* 3.7 23.1 - - + -
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Residues in contact with GLU 101 (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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97D LYS 3.0 13.9 + - - +
98D GLU* 3.2 14.1 + - - +
100D PHE* 1.3 77.5 - - - +
102D LEU* 1.3 72.7 + - + +
104D SER* 3.5 8.7 + - - -
105D GLY* 3.5 7.3 + - - -
224D LEU 4.9 1.1 - - - +
225D GLY* 3.5 31.1 - - - +
226D ALA* 5.4 2.7 - - - -
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Residues in contact with LEU 102 (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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28D VAL* 3.4 28.1 - - + +
31D LYS* 3.7 57.4 - - + +
32D VAL* 3.9 13.9 - - + +
35D THR* 3.8 12.8 - - - +
98D GLU* 3.0 24.5 + - + +
99D ILE* 3.3 7.2 + - + +
101D GLU* 1.3 87.2 - - + +
103D CSS 1.3 62.0 + - - +
105D GLY* 3.1 12.1 + - - -
106D CYS* 3.3 7.1 + - - -
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Residues in contact with CSS 103 (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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32D VAL* 4.2 22.0 - - - -
78D GLN* 5.7 8.3 - - - -
99D ILE* 2.9 33.2 + - + +
100D PHE* 4.2 3.4 - - - +
102D LEU* 1.3 73.6 + - - +
104D SER* 1.3 60.3 + - - +
105D GLY 3.1 0.7 - - - -
106D CYS* 2.9 38.7 + - + +
107D LEU* 2.9 38.7 + - + +
210D PHE* 5.7 9.4 - - + -
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Residues in contact with SER 104 (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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100D PHE* 2.8 47.5 + - - -
101D GLU 3.5 6.1 - - - -
102D LEU 3.2 0.2 - - - -
103D CSS 1.3 78.0 + - - +
105D GLY* 1.3 61.0 + - - +
107D LEU* 3.6 22.2 + - - +
108D GLY 4.4 1.9 + - - -
220D ALA 5.0 1.0 + - - -
223D THR 5.0 1.8 + - - -
224D LEU 3.5 25.4 - - - -
225D GLY* 3.6 5.3 + - - -
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Residues in contact with GLY 105 (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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24D THR* 5.5 6.5 + - - +
28D VAL* 5.4 9.4 - - - -
101D GLU 3.5 5.5 + - - -
102D LEU 3.1 9.1 + - - -
103D CSS 3.1 0.6 - - - -
104D SER* 1.3 80.2 - - - +
106D CYS* 1.3 60.9 + - - +
107D LEU 3.3 0.5 + - - -
108D GLY* 3.5 10.7 + - - -
109D MET* 4.9 0.3 + - - +
224D LEU 5.1 0.8 + - - -
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Residues in contact with CYS 106 (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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24D THR* 5.3 5.8 - - - -
25D MET* 6.5 0.2 - - - -
28D VAL* 3.7 30.3 - - - -
29D GLY* 5.4 2.2 - - - -
32D VAL* 5.1 1.3 - - - -
78D GLN* 6.3 0.4 - - - -
102D LEU 3.3 5.1 + - - -
103D CSS 2.9 40.8 + - + +
105D GLY* 1.3 76.1 - - - +
107D LEU* 1.3 63.1 + - + +
109D MET* 3.0 45.8 + - + +
110D VAL* 3.4 9.9 - - + +
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Residues in contact with LEU 107 (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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100D PHE* 6.1 0.4 - - + -
103D CSS 2.9 22.0 + - + +
104D SER* 3.9 16.8 - - - +
105D GLY 3.3 1.0 - - - -
106D CYS* 1.3 77.1 - - + +
108D GLY* 1.3 60.6 + - - +
109D MET 3.1 1.6 + - - -
110D VAL* 3.1 39.1 + - + +
113D GLY 5.4 0.2 - - - +
114D PRO* 4.8 14.8 - - + -
210D PHE* 4.4 32.5 - - + -
220D ALA 5.8 2.9 - - - +
221D VAL* 6.1 4.9 - - + -
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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