Contacts of the helix formed by residues 97 - 110 (chain D) in PDB entry 1ZQ1
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 ASP 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D THR* 3.7 4.9 - - - -
28D LYS* 3.5 38.7 + - - +
29D LYS 4.0 18.0 - - - +
30D LEU* 3.1 12.6 + - - +
32D SER 5.8 0.2 - - - -
33D PRO* 5.3 1.7 - - - +
94D ARG 5.5 0.9 - - - -
95D GLY* 3.9 0.9 - - - -
96D PRO* 1.3 71.7 - - - +
98D ARG* 1.3 60.7 + - - +
99D GLU* 3.1 15.5 + - - +
100D ALA* 3.0 34.2 + - + +
101D LEU* 2.8 27.7 + - - +
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Residues in contact with ARG 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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95D GLY* 3.9 13.3 + - - -
96D PRO 2.8 26.5 + - - -
97D ASP* 1.3 69.7 + - - +
99D GLU* 1.3 69.4 + - - +
101D LEU* 3.2 9.3 + - + +
102D GLU* 2.9 36.2 + - + +
441D LEU* 3.3 44.8 - - - +
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Residues in contact with GLU 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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26D ASP 3.5 14.6 - - - +
27D THR* 3.4 15.6 - - + -
28D LYS* 5.8 5.5 - - + +
97D ASP* 3.1 10.5 + - - +
98D ARG* 1.3 78.8 - - - +
100D ALA* 1.3 67.6 + - - +
102D GLU* 2.9 10.3 + - - +
103D VAL* 2.8 24.9 + - + +
218D LYS* 3.0 46.8 - - - +
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Residues in contact with ALA 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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25D LEU* 3.5 15.9 - - + +
27D THR* 3.1 29.9 - - - +
30D LEU* 4.0 9.2 - - + -
97D ASP* 3.0 18.1 + - + +
99D GLU* 1.3 77.9 - - - +
101D LEU* 1.3 65.2 + - - +
103D VAL* 3.6 0.6 - - - +
104D ALA* 3.1 16.5 + - - +
161D LEU* 3.7 3.8 - - + +
186D PRO* 3.9 21.1 - - + -
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Residues in contact with LEU 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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96D PRO* 4.7 8.7 - - + +
97D ASP 2.8 22.6 + - - +
98D ARG* 3.4 13.2 - - + +
99D GLU 2.8 1.0 + - - -
100D ALA* 1.3 71.4 - - - +
102D GLU* 1.3 58.7 + - + +
104D ALA* 2.6 33.4 + - - +
105D LEU* 2.9 36.1 + - + -
119D VAL* 6.1 3.6 - - + -
141D ILE* 4.8 10.5 - - + -
161D LEU* 3.6 16.1 - - + +
441D LEU* 3.3 34.5 - - + -
443D ILE* 4.6 13.2 - - + -
447D LEU* 6.0 3.8 - - + -
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Residues in contact with GLU 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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98D ARG* 2.9 32.0 + - + +
99D GLU* 2.9 10.5 + - - +
101D LEU* 1.3 74.3 - - + +
103D VAL* 1.3 64.6 + - + +
105D LEU* 2.7 14.2 + - + +
106D GLN* 2.7 24.9 + - - +
447D LEU* 3.9 27.3 - - + +
451D ILE* 4.2 18.4 - - + +
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Residues in contact with VAL 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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25D LEU* 3.7 19.1 - - + -
27D THR* 4.1 11.0 - - + -
99D GLU* 2.8 27.7 + - + +
100D ALA 3.6 7.4 - - - +
102D GLU* 1.3 72.0 - - + +
104D ALA* 1.3 57.3 + - - +
106D GLN* 3.1 11.6 + - - +
107D ILE* 2.9 47.1 + - + +
216D THR* 4.5 13.5 - - - +
218D LYS* 4.0 43.5 - - + +
219D VAL* 5.2 0.2 - - + -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D LEU* 5.0 1.1 - - + -
100D ALA 3.1 8.4 + - - +
101D LEU 2.6 17.9 + - - +
103D VAL* 1.3 77.0 - - - +
105D LEU* 1.3 59.3 + - - +
107D ILE* 3.1 6.1 + - - +
108D ALA* 2.9 24.0 + - - +
141D ILE* 3.8 30.4 - - + +
159D ILE* 5.1 2.0 - - + +
161D LEU* 4.0 7.0 - - + -
188D ILE* 4.3 23.8 - - + +
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Residues in contact with LEU 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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101D LEU* 2.9 31.3 + - + -
102D GLU* 2.7 12.7 + - - +
104D ALA* 1.3 73.2 - - - +
106D GLN* 1.3 60.4 + - - +
108D ALA* 3.4 6.8 + - - +
109D TYR* 3.0 36.2 + - + +
115D PRO* 3.9 25.6 - - + -
141D ILE* 4.3 9.6 - - + +
443D ILE* 3.6 35.0 - - + -
447D LEU* 4.0 18.6 - - + -
448D LYS* 5.4 1.6 - - + -
451D ILE* 3.6 28.9 - - + -
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Residues in contact with GLN 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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102D GLU 2.7 14.8 + - - +
103D VAL* 3.3 15.2 + - - +
105D LEU* 1.3 71.8 - - - +
107D ILE* 1.3 64.8 + - - +
108D ALA 3.2 0.7 + - - -
109D TYR* 3.2 4.2 + - - +
110D LEU* 3.2 22.9 + - + +
216D THR* 3.2 40.9 + - + +
218D LYS* 6.2 1.2 - - - +
451D ILE* 3.8 17.9 - - + +
454D ASN 4.7 3.8 - - - +
455D LEU* 4.2 7.1 - - + +
456D PRO* 3.2 41.8 - - + +
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Residues in contact with ILE 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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25D LEU* 4.5 9.9 - - + -
103D VAL* 2.9 34.6 + - + +
104D ALA* 3.7 6.3 - - - +
106D GLN* 1.3 75.2 - - - +
108D ALA* 1.3 61.7 + - - +
110D LEU* 3.5 10.3 + - - +
111D LEU* 3.1 37.3 + - + +
159D ILE* 5.5 2.2 - - + -
188D ILE* 4.1 22.2 - - + -
190D ILE* 4.4 4.5 - - + -
212D ALA* 4.8 4.5 - - + +
213D LEU* 3.2 37.9 - - + -
216D THR* 3.5 19.5 - - + -
219D VAL* 4.8 3.6 - - + -
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Residues in contact with ALA 108 (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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104D ALA 2.9 12.9 + - - +
105D LEU* 3.4 14.8 - - - +
106D GLN 3.1 0.2 - - - -
107D ILE* 1.3 75.7 - - - +
109D TYR* 1.3 62.7 + - - +
111D LEU* 3.0 6.9 + - - -
113D ALA* 2.9 30.7 + - + +
115D PRO* 4.7 5.8 - - + -
141D ILE* 5.3 1.6 - - + -
142D ALA* 3.7 30.3 - - + -
159D ILE* 3.8 16.3 - - + +
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B GLU* 4.5 1.6 + - - -
105D LEU* 3.0 29.6 + - + -
106D GLN 3.2 2.0 + - - +
108D ALA* 1.3 71.9 - - - +
110D LEU* 1.3 55.5 + - - +
111D LEU 2.7 6.7 + - - -
112D ASN* 2.7 29.0 + - - +
113D ALA 4.1 9.6 - - - +
115D PRO* 3.3 38.4 - - + +
448D LYS* 3.3 46.9 + - - +
451D ILE* 4.2 11.0 - - + -
452D LYS* 3.6 48.0 - - + +
455D LEU* 3.6 27.0 - - + +
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Residues in contact with LEU 110 (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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106D GLN* 3.2 21.0 + - + +
107D ILE* 3.5 15.3 - - - +
109D TYR* 1.3 77.2 - - - +
111D LEU* 1.3 64.6 + - - +
112D ASN* 3.5 3.9 + - - +
208D PHE* 3.3 20.1 - - - -
212D ALA* 3.1 40.6 - - + +
215D ALA* 4.1 10.3 - - + -
216D THR* 4.2 8.3 - - + -
455D LEU* 3.7 34.8 - - + -
456D PRO* 4.2 8.7 - - + +
458D LEU* 4.0 20.9 - - + +
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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