Contacts of the helix formed by residues 84 - 94 (chain D) in PDB entry 1QDV
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 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D ASN* 2.9 27.5 + - - -
82D ARG 3.2 0.2 + - - -
83D PRO* 1.3 76.7 - - - +
85D PHE* 1.3 63.5 + - - +
87D ALA* 3.2 16.0 + - - +
88D ILE* 3.2 14.2 + - - +
101D PRO* 5.2 0.7 - - - -
104D VAL* 3.4 21.5 - - - +
108D ILE* 4.1 0.2 - - - +
109D PHE* 3.5 20.9 - - - -
112D GLU* 3.5 29.1 - - - +
116D TYR* 6.0 0.9 - - - -
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Residues in contact with PHE 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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37D ILE* 3.9 23.3 - - + -
39D ILE* 3.6 20.0 - - + -
44D PHE* 3.7 44.6 - + + -
59D LEU* 3.9 19.3 - - + -
81D ASN 4.2 5.6 + - - +
82D ARG 3.1 13.8 + - - +
84D SER* 1.3 77.4 - - - +
86D ASP* 1.3 64.7 + - - +
88D ILE* 3.8 25.4 - - + -
89D LEU* 2.8 38.4 + - + +
116D TYR* 3.7 37.0 - + + -
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Residues in contact with ASP 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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81A ASN* 4.6 7.6 + - - +
82A ARG* 3.7 12.5 + - - +
83A PRO* 3.5 37.6 - - + +
42D LEU* 5.9 1.4 - - - +
44D PHE* 3.5 25.8 - - - -
82D ARG 4.3 2.9 + - - +
83D PRO* 3.8 15.2 + - - +
84D SER 3.3 0.6 - - - -
85D PHE* 1.3 75.1 - - - +
87D ALA* 1.3 58.4 + - - +
89D LEU* 3.5 4.2 + - - +
90D TYR* 2.9 27.9 + - - +
93D GLN* 5.0 0.7 - - - +
101D PRO* 5.8 2.9 - - + -
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Residues in contact with ALA 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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83D PRO 4.7 0.2 + - - -
84D SER 3.2 9.6 + - - +
86D ASP* 1.3 78.8 - - - +
88D ILE* 1.3 65.0 + - - +
90D TYR* 3.7 8.3 - - - +
91D TYR* 3.1 21.8 + - - +
97D ARG 4.7 1.7 - - - +
98D LEU* 4.5 4.3 - - - +
99D ARG* 3.1 28.6 + - + +
101D PRO* 3.8 15.0 - - + +
109D PHE* 3.6 17.9 - - + -
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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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59D LEU* 4.7 1.3 - - + -
84D SER 3.2 15.3 + - - +
85D PHE* 3.2 31.7 + - + +
87D ALA* 1.3 74.3 - - - +
89D LEU* 1.3 63.0 + - - +
91D TYR* 3.1 22.7 - - - +
92D TYR* 3.3 21.8 - - + -
98D LEU* 4.9 0.4 - - + -
109D PHE* 4.3 17.9 - - + -
112D GLU* 4.4 3.6 - - + -
113D ILE* 4.3 15.3 - - + +
116D TYR* 4.0 39.5 - - + -
118D LEU* 4.1 22.0 - - + -
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Residues in contact with LEU 89 (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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40A SER* 4.1 13.7 - - - -
82A ARG* 5.1 1.8 - - - -
37D ILE* 5.4 1.8 - - + -
44D PHE* 3.9 30.5 - - + -
45D GLU 5.0 0.2 - - - +
46D THR* 3.9 34.8 - - + +
51D LEU* 4.8 10.1 - - + -
59D LEU* 6.4 0.2 - - + -
85D PHE* 2.8 33.0 + - + +
86D ASP* 3.8 4.5 - - - +
88D ILE* 1.3 77.9 - - - +
90D TYR* 1.3 61.3 + - - +
92D TYR* 3.1 11.3 + - + +
93D GLN* 3.0 44.2 + - + +
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Residues in contact with TYR 90 (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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81A ASN* 4.1 26.2 - - + +
108A ILE* 3.6 51.8 - - + +
111A GLU* 3.4 23.7 + - - +
112A GLU* 4.9 7.2 + - - -
86D ASP 2.9 19.1 + - - +
87D ALA* 3.7 9.2 - - - +
88D ILE 3.3 0.2 - - - -
89D LEU* 1.3 73.1 - - - +
91D TYR* 1.3 54.6 + - - +
93D GLN* 3.5 19.7 + - + +
94D SER* 2.7 64.3 + - - -
97D ARG* 3.8 21.2 + - + -
99D ARG* 4.9 3.6 - - + -
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Residues in contact with TYR 91 (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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54D PHE* 3.9 42.1 - + + -
57D THR* 5.0 2.0 - - + -
87D ALA 3.1 11.3 + - - +
88D ILE 3.1 12.1 - - - +
90D TYR* 1.3 77.9 - - - +
92D TYR* 1.3 67.8 + + - +
95D GLY 3.4 0.2 + - - -
96D GLY* 2.8 62.3 + - - -
97D ARG 3.3 14.5 + - - +
98D LEU* 3.8 26.0 - - + -
118D LEU* 3.9 38.0 + - + -
122D ALA* 3.6 30.1 - - + +
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Residues in contact with TYR 92 (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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50D THR* 3.6 31.2 - - + +
51D LEU* 3.7 31.4 - - + -
53D GLN* 2.7 23.6 - - - +
54D PHE* 3.7 23.3 - + + -
57D THR* 2.6 37.2 + - + +
59D LEU* 3.6 31.2 + - + +
60D GLY 4.5 1.8 - - - -
88D ILE* 3.3 21.8 - - + -
89D LEU* 3.1 11.0 + - + +
91D TYR* 1.3 81.9 - + - +
93D GLN* 1.3 65.4 + - - +
95D GLY* 3.0 9.7 + - - -
116D TYR* 4.6 1.6 + - - +
118D LEU* 3.8 21.7 - - + +
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Residues in contact with GLN 93 (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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40A SER* 2.9 28.5 + - - -
79A ASP* 3.0 40.2 + - - +
80A ARG* 3.4 12.8 + - - +
81A ASN* 4.1 2.3 + - - -
50D THR* 4.0 13.9 - - + -
53D GLN* 5.4 1.4 + - - -
86D ASP 5.0 0.5 - - - +
89D LEU* 3.0 32.7 + - + +
90D TYR* 3.5 32.1 + - + +
92D TYR* 1.3 78.2 - - - +
94D SER* 1.3 59.0 + - - +
95D GLY 3.5 0.5 + - - -
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Residues in contact with SER 94 (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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111A GLU* 5.8 0.7 - - - -
90D TYR* 2.7 52.5 + - - -
91D TYR 3.4 1.0 + - - -
93D GLN* 1.3 72.5 - - - +
95D GLY* 1.3 60.6 + - - +
97D ARG* 2.9 41.4 + - - +
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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