Contacts of the helix formed by residues 100 - 121 (chain D) in PDB entry 6G0L
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 100 (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* 5.3 15.3 - - + +
95C LYS* 5.6 10.1 - - + -
96C LEU* 5.9 2.9 - - + +
98D LEU 4.7 0.2 - - - +
99D LEU* 1.4 103.8 - - + +
101D GLY* 1.3 66.3 + - - +
102D GLU 3.3 2.5 + - - -
103D LEU* 3.5 8.6 + - + +
104D ALA* 3.2 19.6 + - - +
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 5.9 4.0 - - - -
99D LEU 4.1 0.2 + - - -
100D PRO* 1.3 73.9 - - - +
102D GLU* 1.3 63.3 + - - +
104D ALA* 3.6 4.8 + - - +
105D LYS* 3.2 32.9 + - - +
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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
----------------------------------------------------------
92C GLU* 6.4 2.0 - - + -
100D PRO 3.3 0.6 + - - -
101D GLY* 1.3 74.7 - - - +
103D LEU* 1.4 66.5 + - - +
104D ALA 3.2 1.3 + - - -
105D LYS* 3.2 36.9 + - - +
106D HIS* 3.8 29.0 + - + -
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Residues in contact with LEU 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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57C TYR* 4.0 28.0 + - + +
58C LEU* 4.4 13.5 - - + -
61C GLU* 5.4 6.7 - - + -
92C GLU* 5.5 17.2 - - + +
93C LEU* 5.1 13.7 - - + -
96C LEU* 6.4 0.9 - - + -
99D LEU* 3.6 37.7 - - + -
100D PRO* 3.5 11.0 + - + +
102D GLU* 1.4 76.2 - - - +
104D ALA* 1.3 57.5 - - - +
106D HIS* 3.3 4.7 + - - +
107D ALA* 2.8 49.7 + - + +
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Residues in contact with ALA 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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67B ARG* 5.0 4.3 - - - +
95D VAL* 5.1 3.7 - - - +
96D ARG* 4.4 17.0 - - + +
99D LEU* 4.1 20.2 - - + +
100D PRO 3.2 16.7 + - - +
101D GLY* 3.7 7.4 - - - +
102D GLU 3.2 0.4 - - - -
103D LEU* 1.3 88.8 - - - +
105D LYS* 1.3 63.4 + - + +
107D ALA* 3.3 4.0 + - - +
108D VAL* 3.0 28.7 + - + +
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Residues in contact with LYS 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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96D ARG* 6.3 1.3 - - - +
101D GLY 3.2 15.9 + - - +
102D GLU* 3.2 42.2 + - - +
103D LEU 3.2 0.4 - - - -
104D ALA* 1.3 78.4 - - + +
106D HIS* 1.3 64.7 + - + +
108D VAL* 3.3 9.5 + - - +
109D SER* 2.3 36.2 + - - +
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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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57C TYR* 4.2 19.6 + - + +
102D GLU* 3.8 24.4 + - + +
103D LEU* 3.3 7.2 + - - +
105D LYS* 1.3 87.0 + - + +
107D ALA* 1.3 64.4 + - - +
109D SER* 3.2 8.9 + - - -
110D GLU* 3.0 26.1 + - - +
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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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54C VAL* 4.5 19.3 - - + +
57C TYR* 4.3 19.5 - - + -
95D VAL* 5.2 7.2 - - + -
103D LEU* 2.8 35.2 + - + +
104D ALA* 3.5 6.5 - - - +
105D LYS 3.1 0.2 - - - -
106D HIS* 1.3 78.5 - - - +
108D VAL* 1.4 61.7 + - - +
110D GLU* 3.6 9.3 + - - +
111D GLY* 3.0 17.8 + - - -
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Residues in contact with VAL 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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50C TYR* 4.1 19.3 + - - +
92D GLN* 4.1 20.6 - - + +
95D VAL* 5.9 5.8 - - + +
96D ARG* 4.1 37.5 - - + +
104D ALA* 3.0 27.8 + - + +
105D LYS* 3.7 8.5 - - - +
106D HIS 3.3 0.2 - - - -
107D ALA* 1.4 76.1 - - - +
109D SER* 1.3 56.4 + - - +
111D GLY* 2.9 2.5 + - - -
112D THR* 2.6 38.9 + - + -
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Residues in contact with SER 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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105D LYS* 2.3 28.2 + - - +
106D HIS* 3.4 10.4 - - - -
108D VAL* 1.3 80.1 - - - +
110D GLU* 1.3 61.9 + - - +
112D THR* 2.8 29.4 - - - +
113D LYS* 3.1 11.9 + - - +
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Residues in contact with GLU 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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23C LEU* 3.8 16.5 - - - +
53C ALA* 3.3 36.9 - - - +
54C VAL* 4.1 3.3 + - - -
56C GLU* 4.5 3.4 - - - +
57C TYR* 4.5 20.4 - - + +
106D HIS 3.0 15.7 + - - +
107D ALA* 3.6 8.5 - - - +
109D SER* 1.3 78.5 - - - +
111D GLY* 1.3 86.0 + - - +
113D LYS* 4.1 6.6 - - - +
114D ALA* 3.1 20.1 + - - +
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Residues in contact with GLY 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* 3.7 18.2 - - - -
53C ALA* 4.3 10.1 - - - +
54C VAL* 5.4 2.7 - - - -
107D ALA 3.0 7.4 + - - -
108D VAL 2.9 7.0 + - - -
110D GLU* 1.3 93.8 + - - +
112D THR* 1.3 62.5 + - - +
113D LYS 3.5 0.3 + - - -
114D ALA* 3.6 1.6 + - - +
115D VAL* 3.4 26.2 + - - +
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Residues in contact with THR 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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50C TYR* 4.2 9.1 - - - -
92D GLN* 4.7 10.4 + - - -
108D VAL* 2.6 23.7 + - + +
109D SER* 2.8 33.2 - - - +
111D GLY* 1.3 75.5 - - - +
113D LYS* 1.3 60.7 + - + +
115D VAL* 3.6 3.6 + - - +
116D THR* 2.4 39.3 + - - +
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Residues in contact with LYS 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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109D SER 3.1 14.7 + - - +
110D GLU* 4.1 5.6 - - - +
112D THR* 1.3 81.1 - - + +
114D ALA* 1.4 70.5 + - - +
115D VAL 3.0 2.5 - - - -
116D THR* 3.0 7.8 + - - -
117D LYS* 2.8 29.1 + - + +
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Residues in contact with ALA 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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21C ALA* 3.0 24.4 - - - +
23C LEU* 3.6 39.0 - - + -
49C VAL* 5.4 1.3 - - + -
53C ALA* 4.1 2.7 - - + -
110D GLU* 3.1 24.1 + - - +
111D GLY 4.0 4.3 - - - +
112D THR 3.5 0.2 - - - -
113D LYS* 1.4 80.4 - - - +
115D VAL* 1.3 62.0 + - + +
117D LYS* 3.6 3.8 + - - +
118D TYR* 3.1 11.8 + - - +
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Residues in contact with VAL 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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46C GLY* 4.5 11.0 - - - +
49C VAL* 4.1 12.1 - - + +
50C TYR* 3.7 41.3 - - + +
88D SER* 5.9 2.0 - - - +
111D GLY 3.4 15.2 + - - +
112D THR* 3.9 5.8 - - - +
113D LYS 3.0 1.0 - - - -
114D ALA* 1.3 77.1 - - + +
116D THR* 1.3 69.6 + - - +
118D TYR* 2.9 22.5 + - + +
119D THR* 2.9 16.0 + - - -
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Residues in contact with THR 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 THR* 2.4 27.6 + - - +
113D LYS* 3.3 10.5 - - - -
115D VAL* 1.3 81.3 - - - +
117D LYS* 1.3 57.7 + - - +
119D THR* 2.8 32.3 - - + +
120D SER* 2.9 15.0 + - - +
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Residues in contact with LYS 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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19C SER 5.4 1.3 - - - -
20C ARG 4.1 5.1 - - - +
21C ALA 3.6 18.4 - - - +
22C GLY* 4.0 18.1 + - - -
113D LYS* 2.8 21.4 + - + +
114D ALA* 3.8 5.6 - - - +
116D THR* 1.3 73.8 - - - +
118D TYR* 1.3 67.7 + - - +
120D SER* 3.0 19.7 + - - -
121D ALA* 3.1 13.2 + - + +
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Residues in contact with TYR 118 (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* 5.0 8.2 - - + +
20C ARG* 3.3 35.8 + - + -
21C ALA* 3.5 28.7 - - + -
27C VAL* 6.3 2.0 - - + -
49C VAL* 4.3 24.0 - - + -
114D ALA 3.1 14.3 + - - +
115D VAL* 2.9 21.6 + - + +
117D LYS* 1.3 78.0 - - - +
119D THR* 1.3 61.8 + - - +
121D ALA* 2.8 24.4 + - - +
122D LYS* 5.9 7.0 - - + +
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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 VAL* 2.9 12.6 + - + +
116D THR* 2.8 34.1 - - + +
118D TYR* 1.3 79.4 - - - +
120D SER* 1.3 61.0 + - - +
121D ALA 2.2 24.6 - - - +
122D LYS* 3.6 14.5 + - - +
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Residues in contact with SER 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D THR* 2.9 19.4 + - - +
117D LYS* 3.0 13.4 + - - -
119D THR* 1.3 83.3 - - - +
121D ALA* 1.3 60.1 + - - +
122D LYS* 4.9 0.3 - - - +
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Residues in contact with ALA 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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20C ARG* 4.3 24.7 - - + +
117D LYS* 3.1 8.2 + - + +
118D TYR* 2.8 20.3 - - - +
119D THR 2.2 23.7 - - - +
120D SER* 1.3 77.4 - - - +
122D LYS* 1.4 61.9 + - - +
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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
------------------------------------------------------------
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