Contacts of the helix formed by residues 97 - 114 (chain D) in PDB entry 5HZZ
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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11D ALA* 5.0 1.9 - - - +
27D GLU 5.8 0.6 + - - -
95D GLY 4.0 2.6 + - - -
96D ILE* 1.3 69.2 - - - +
98D ALA* 1.3 64.1 + - - +
99D ASP* 2.8 26.0 + - - +
100D ALA* 3.2 23.4 + - + +
101D VAL* 3.3 16.8 + - - +
141D LEU* 3.7 28.4 - - + +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.7 1.4 - - + +
11D ALA* 3.9 9.3 - - + +
88D TYR* 3.5 32.5 - - + +
91D LEU* 3.5 35.6 - - + +
92D ASP 5.8 0.2 - - - +
96D ILE 3.0 6.5 + - - -
97D ASP* 1.3 73.0 + - - +
99D ASP* 1.3 58.6 + - - +
101D VAL* 3.8 3.4 - - - +
102D PHE* 2.8 32.3 + - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.0 32.0 + - - +
13B ARG* 5.7 2.3 - - - +
9D THR* 2.7 39.3 + - - +
10D ASN 5.4 0.2 + - - -
11D ALA* 3.6 17.2 - - - +
12D GLU* 4.7 4.2 - - - +
88D TYR* 4.3 0.7 + - - -
97D ASP* 2.8 11.3 + - - +
98D ALA* 1.3 78.9 - - - +
100D ALA* 1.3 56.0 + - - +
102D PHE* 3.9 0.7 - - - +
103D ALA* 2.9 31.5 + - - +
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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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97D ASP* 3.2 25.2 + - - +
99D ASP* 1.3 79.5 - - - +
101D VAL* 1.3 62.0 + - - +
103D ALA* 3.5 6.9 + - - +
104D GLU* 3.3 18.2 + - - +
137D VAL* 3.8 23.4 - - + +
141D LEU* 4.1 13.5 - - + -
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Residues in contact with VAL 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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77B ALA* 3.7 15.5 - - + +
81B ALA* 3.6 22.4 - - + -
91D LEU* 5.1 3.4 - - + -
96D ILE* 3.5 24.2 - - + -
97D ASP 3.3 15.5 + - - +
98D ALA* 3.9 7.4 - - - +
100D ALA* 1.3 74.0 - - - +
102D PHE* 1.3 66.2 + - - +
104D GLU* 3.1 6.8 + - - +
105D VAL* 3.0 20.7 + - + +
134D VAL* 3.9 29.1 - - + +
137D VAL* 4.0 18.2 - - + -
138D ILE* 5.3 0.7 - - + -
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Residues in contact with PHE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.2 47.3 - - + +
13B ARG* 3.8 22.2 - - + -
14B LEU* 3.6 17.7 - - + -
81B ALA* 4.2 12.9 - - + +
84B LEU* 3.9 31.6 - - + -
85B TYR* 3.5 36.6 - + - -
88B TYR* 4.0 17.3 - + - -
98D ALA 2.8 19.2 + - - +
99D ASP 3.9 2.0 - - - +
101D VAL* 1.3 75.5 - - - +
103D ALA* 1.3 54.5 + - - +
104D GLU 3.1 0.2 + - - -
105D VAL* 3.1 3.5 + - + +
106D HIS* 2.7 33.3 + - + +
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Residues in contact with ALA 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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10B ASN* 5.2 0.2 + - - -
13B ARG* 4.7 20.4 - - - +
99D ASP 2.9 20.4 + - - +
100D ALA* 3.6 8.1 - - - +
101D VAL 3.2 0.2 - - - -
102D PHE* 1.3 78.4 - - - +
104D GLU* 1.3 57.3 + - - +
106D HIS* 3.8 7.8 - - - +
107D ARG* 2.9 27.4 + - - +
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Residues in contact with GLU 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 ALA 3.3 2.7 + - - +
101D VAL* 3.1 10.3 + - - +
103D ALA* 1.3 77.2 - - - +
105D VAL* 1.3 66.1 + - - +
107D ARG* 2.8 42.5 + - - +
108D ALA* 3.1 21.5 + - - +
130D ARG* 4.8 3.9 + - - -
132D ALA* 3.9 4.7 - - + -
133D ASP* 2.8 44.1 + - - +
134D VAL* 4.5 2.7 - - + +
137D VAL* 3.7 28.4 - - + +
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Residues in contact with VAL 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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78B HIS* 4.0 20.2 - - + +
81B ALA* 3.9 22.9 - - + +
82B ASP* 3.6 22.4 - - - +
85B TYR* 3.8 16.6 - - + -
101D VAL 3.0 16.0 + - - +
102D PHE* 3.7 8.3 - - + +
104D GLU* 1.3 73.8 - - - +
106D HIS* 1.3 58.3 + - - +
108D ALA* 3.3 2.9 + - - +
109D ASN* 2.9 46.5 + - - +
132D ALA* 4.1 11.0 - - + -
134D VAL* 4.7 4.9 - - + -
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Residues in contact with HIS 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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13B ARG* 3.2 58.4 - - + +
16B GLU* 3.4 19.5 + - - -
17B PHE* 4.2 5.8 - - + -
85B TYR* 2.7 38.8 + - + -
102D PHE* 2.7 26.6 + - + +
103D ALA 3.8 4.9 - - - +
105D VAL* 1.3 71.1 - - - +
107D ARG* 1.3 60.8 + - - +
110D LEU* 2.8 58.1 + - + +
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Residues in contact with ARG 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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103D ALA 2.9 19.5 + - - +
104D GLU* 2.8 40.7 + - - +
106D HIS* 1.3 78.1 - - - +
108D ALA* 1.3 68.1 + - - +
110D LEU* 4.0 3.8 - - - +
111D SER* 2.8 43.0 + - - -
130D ARG* 3.0 73.2 + - - +
131D PRO 3.0 12.9 + - - -
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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 GLU 3.1 12.9 + - - +
105D VAL 3.8 4.0 - - - +
107D ARG* 1.3 89.3 - - - +
109D ASN* 1.3 60.9 + - - +
111D SER* 4.3 0.2 - - - -
112D LYS* 2.9 25.1 + - - +
129D TRP* 3.0 21.8 + - + +
130D ARG 3.9 8.7 - - - +
131D PRO 3.9 0.2 - - - -
132D ALA* 3.5 32.1 - - + +
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Residues in contact with ASN 109 (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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17B PHE* 3.7 21.9 - - + -
82B ASP* 5.2 1.8 + - - -
85B TYR* 3.5 43.0 - - - +
105D VAL* 2.9 33.6 + - - +
106D HIS 3.9 0.2 - - - +
108D ALA* 1.3 75.7 - - - +
110D LEU* 1.3 66.7 + - - +
112D LYS* 3.3 9.8 + - - +
113D ALA 3.1 16.8 + - - -
129D TRP* 5.9 1.0 - - - -
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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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16B GLU* 3.3 27.8 - - + +
17B PHE* 4.1 21.2 - - + -
20B ALA* 3.6 31.0 - - + -
106D HIS* 2.8 44.8 + - + +
107D ARG* 4.0 3.8 - - - +
109D ASN* 1.3 73.0 - - - +
111D SER* 1.3 61.9 + - - +
113D ALA* 3.1 15.3 + - + +
114D SER* 3.3 11.1 + - - -
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Residues in contact with SER 111 (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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107D ARG* 2.8 32.5 + - - -
108D ALA* 3.7 5.6 - - - -
110D LEU* 1.3 77.2 - - - +
112D LYS* 1.3 61.2 + - - +
114D SER* 2.6 28.3 + - - -
126D PRO* 3.2 11.8 - - - +
129D TRP* 3.1 20.6 - - - -
130D ARG 5.1 0.3 + - - -
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Residues in contact with LYS 112 (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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108D ALA 2.9 18.6 + - - +
109D ASN* 3.3 10.7 + - - +
111D SER* 1.3 75.9 - - - +
113D ALA* 1.3 60.6 + - - +
115D GLY* 3.1 10.9 + - - -
124D LEU* 3.3 24.2 + - - +
125D LYS* 4.0 39.0 - - + +
126D PRO* 3.8 2.9 - - - +
129D TRP* 3.3 20.1 - - + +
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Residues in contact with ALA 113 (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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17B PHE* 4.6 3.4 - - + -
20B ALA* 4.6 19.5 - - + +
21B ILE* 3.7 30.2 - - + -
109D ASN 3.1 12.0 + - - +
110D LEU* 3.1 14.1 + - - +
112D LYS* 1.3 72.6 - - - +
114D SER* 1.3 56.1 + - - +
115D GLY* 3.1 10.8 + - - -
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Residues in contact with SER 114 (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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110D LEU 3.3 8.1 + - - -
111D SER* 2.6 22.5 + - - -
113D ALA* 1.3 74.9 - - - +
115D GLY* 1.3 61.9 + - - +
126D PRO* 3.6 14.4 - - - +
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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