Contacts of the helix formed by residues 103 - 123 (chain D) in PDB entry 3AZL
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 PRO 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C GLU* 3.4 44.0 - - + +
95C LYS* 4.6 14.6 - - + -
96C LEU* 4.3 20.2 - - + +
101D LEU 3.8 5.6 - - - +
102D LEU* 1.3 88.0 - - + +
104D GLY* 1.3 69.1 + - - +
105D GLU 3.2 0.6 + - - -
106D LEU* 3.0 22.6 + - + +
107D ALA 3.2 3.8 + - - -
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 3.9 4.7 + - - -
102D LEU 3.9 2.0 + - - -
103D PRO* 1.3 68.3 - - - +
105D GLU* 1.3 65.4 + - - -
107D ALA* 3.0 17.5 + - - +
108D LYS* 3.2 23.3 + - - +
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 5.0 0.7 - - - -
92C GLU* 3.1 22.1 + - - +
104D GLY* 1.3 71.0 - - - -
106D LEU* 1.3 62.6 + - - +
108D LYS* 3.1 35.8 + - - +
109D HIS* 3.0 51.8 + - + +
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Residues in contact with LEU 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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57C TYR* 3.5 28.9 - - + +
58C LEU* 3.7 15.0 - - + -
61C GLU* 4.0 23.1 - - + -
90C ASP* 5.6 1.3 - - - +
92C GLU* 3.2 33.5 + - + +
93C LEU* 3.7 26.7 - - + +
96C LEU* 4.3 13.5 - - + -
102D LEU* 4.0 9.3 - - + +
103D PRO* 3.0 15.3 + - + +
105D GLU* 1.3 77.6 - - - +
107D ALA* 1.3 57.9 + - - +
110D ALA* 3.0 30.8 + - - +
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Residues in contact with ALA 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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98D VAL* 4.4 9.9 - - + +
99D ARG* 4.6 15.0 - - + +
102D LEU* 3.7 34.0 - - + +
103D PRO 3.2 1.6 + - - -
104D GLY* 3.0 11.9 + - - +
106D LEU* 1.3 76.9 - - - +
108D LYS* 1.3 56.7 + - + +
110D ALA* 3.1 2.7 + - - +
111D VAL* 2.8 40.2 + - - +
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Residues in contact with LYS 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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99D ARG* 5.3 6.0 - - - +
104D GLY* 3.2 16.9 + - - +
105D GLU* 3.1 35.6 + - - +
107D ALA* 1.3 78.8 - - + +
109D HIS* 1.3 69.5 + - + +
111D VAL* 3.5 7.0 + - - +
112D SER* 3.1 25.1 + - - -
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Residues in contact with HIS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 3.1 40.5 + - + +
61C GLU* 5.3 1.6 + - - -
105D GLU* 3.0 38.4 + - + +
108D LYS* 1.3 79.8 - - + +
110D ALA* 1.3 63.6 + - - +
112D SER* 3.1 8.3 + - - -
113D GLU* 3.0 26.5 + - + +
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Residues in contact with ALA 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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54C VAL* 3.6 30.5 - - + +
57C TYR* 3.6 23.6 - - + -
98D VAL* 4.1 4.3 - - + -
102D LEU* 4.0 17.9 - - + -
106D LEU 3.0 19.7 + - - +
107D ALA 3.8 2.5 - - - +
109D HIS* 1.3 75.1 - - - +
111D VAL* 1.3 57.8 + - - +
113D GLU* 3.4 2.2 + - - +
114D GLY 2.9 25.6 + - - -
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Residues in contact with VAL 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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50C TYR* 3.4 21.0 + - - +
95D GLN* 3.7 12.8 - - + +
98D VAL* 4.1 15.7 - - + -
99D ARG* 3.6 47.6 - - + +
107D ALA 2.8 20.7 + - - +
108D LYS* 3.7 5.6 - - - +
109D HIS 3.2 0.2 - - - -
110D ALA* 1.3 77.5 - - - +
112D SER* 1.3 62.3 + - - +
115D THR* 2.9 33.3 + - - +
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Residues in contact with SER 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 LYS 3.1 13.7 + - - -
109D HIS* 3.1 12.5 + - - -
111D VAL* 1.3 79.6 - - - +
113D GLU* 1.3 59.1 + - - +
115D THR* 3.7 3.9 - - - -
116D LYS* 2.8 33.2 + - - +
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Residues in contact with GLU 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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53C ALA* 3.8 12.9 - - + +
57C TYR* 3.9 39.7 - - + +
109D HIS* 3.0 16.4 + - + +
110D ALA 3.8 3.4 - - - +
112D SER* 1.3 77.8 - - - +
114D GLY* 1.3 57.1 + - - +
116D LYS* 3.4 33.1 + - - +
117D ALA* 2.9 31.9 + - - +
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Residues in contact with GLY 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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50C TYR* 3.7 30.1 - - - -
53C ALA* 4.0 12.5 - - - +
54C VAL* 4.7 0.2 - - - -
110D ALA 2.9 16.7 + - - -
112D SER 3.2 0.2 - - - -
113D GLU* 1.3 77.1 - - - +
115D THR* 1.3 62.1 + - - +
117D ALA* 3.2 4.0 + - - +
118D VAL* 3.0 26.9 + - - +
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Residues in contact with THR 115 (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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50C TYR* 3.7 5.4 - - - -
95D GLN* 3.4 20.8 + - - +
111D VAL* 2.9 20.3 + - - +
112D SER* 3.7 4.5 - - - -
114D GLY* 1.3 71.3 - - - +
116D LYS* 1.3 67.7 + - - +
118D VAL* 3.0 6.1 + - + +
119D THR* 2.9 39.4 + - + +
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Residues in contact with LYS 116 (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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112D SER 2.8 21.3 + - - +
113D GLU* 3.4 28.5 + - - +
115D THR* 1.3 73.8 - - - +
117D ALA* 1.3 64.6 + - - +
119D THR* 3.2 8.7 + - - +
120D LYS* 3.1 26.6 + - + +
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Residues in contact with ALA 117 (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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21C ALA* 3.8 20.5 - - - +
23C LEU* 4.1 7.9 - - + -
49C VAL* 3.7 17.1 - - + +
53C ALA* 3.7 19.5 - - + -
113D GLU 2.9 18.3 + - - +
114D GLY 3.6 3.8 - - - +
116D LYS* 1.3 79.1 - - - +
118D VAL* 1.3 58.2 + - - +
120D LYS* 3.4 1.7 + - - +
121D TYR* 2.9 30.1 + - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY* 3.8 32.1 - - - +
49C VAL* 4.2 6.5 - - + -
50C TYR* 3.8 24.2 - - + +
91D SER* 4.2 11.7 - - - +
114D GLY 3.0 17.1 + - - +
115D THR* 3.0 9.2 + - + +
117D ALA* 1.3 74.1 - - - +
119D THR* 1.3 68.7 + - + +
121D TYR* 3.1 4.1 + - + +
122D THR* 2.8 41.2 + - + +
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Residues in contact with THR 119 (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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115D THR* 2.9 33.9 + - + +
116D LYS* 3.2 14.6 + - - +
118D VAL* 1.3 74.5 - - + +
120D LYS* 1.3 65.4 + - - +
122D THR* 3.0 21.5 + - - -
123D SER* 3.1 15.6 + - - -
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Residues in contact with LYS 120 (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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19C SER 3.6 13.7 + - - -
20C ARG* 3.4 18.3 + - - +
21C ALA 3.6 19.1 - - - +
22C GLY* 3.8 11.4 - - - +
116D LYS* 3.1 18.0 + - + +
117D ALA 3.7 4.0 - - - +
118D VAL 3.1 1.0 - - - -
119D THR* 1.3 82.3 + - - +
121D TYR* 1.3 62.7 + - - +
123D SER* 3.1 23.8 + - - -
124D ALA 3.9 2.1 + - - -
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Residues in contact with TYR 121 (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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17C ARG* 3.2 54.7 + - + +
20C ARG* 3.5 39.0 + - + -
21C ALA* 4.1 2.7 - - + -
45C ALA* 4.6 20.4 - - + +
46C GLY* 5.3 4.5 - - - -
49C VAL* 3.8 29.4 - - + -
117D ALA 2.9 17.9 + - - +
118D VAL* 3.5 4.3 - - + +
120D LYS* 1.3 78.3 - - - +
122D THR* 1.3 68.5 + - + +
124D ALA* 3.2 16.3 + - - -
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Residues in contact with THR 122 (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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118D VAL* 2.8 32.0 + - + +
119D THR* 3.0 18.2 + - - -
121D TYR* 1.3 79.8 - - + +
123D SER* 1.3 53.7 + - - +
124D ALA* 2.7 18.4 + - - +
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Residues in contact with SER 123 (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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119D THR 3.1 11.9 + - - -
120D LYS* 3.1 16.7 + - - -
122D THR* 1.3 76.6 + - - +
124D ALA* 1.3 68.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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