Contacts of the helix formed by residues 104 - 124 (chain D) in PDB entry 6R90
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 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C GLU* 3.6 43.2 - - + +
96C LYS* 4.6 15.3 - - + -
97C LEU* 5.6 7.0 - - + -
102D LEU 4.1 4.3 - - - +
103D LEU* 1.3 90.0 - - + +
105D GLY* 1.3 67.7 + - - +
106D GLU 3.4 1.6 + - - -
107D LEU* 3.4 17.6 + - + +
108D ALA* 3.5 4.9 + - - -
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Residues in contact with GLY 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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93C GLU* 3.9 4.0 - - - -
103D LEU 4.0 1.0 + - - -
104D PRO* 1.3 70.7 - - - +
106D GLU* 1.3 62.2 + - - -
108D ALA* 2.9 23.7 + - - +
109D LYS* 3.0 21.7 + - - +
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Residues in contact with GLU 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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93C GLU* 3.1 17.1 + - - +
105D GLY* 1.3 73.0 - - - -
107D LEU* 1.3 63.7 + - - +
109D LYS* 3.1 36.4 + - - +
110D HIS* 3.0 44.8 + - + +
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Residues in contact with LEU 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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58C TYR* 3.9 27.4 - - + +
59C LEU* 3.6 29.4 - - + -
62C GLU* 4.4 15.3 - - + -
91C ASP* 6.0 0.4 - - - +
93C GLU* 3.3 24.4 + - + +
94C LEU* 4.0 28.5 - - + -
97C LEU* 5.1 3.6 - - + -
103D LEU* 4.3 17.0 - - + -
104D PRO* 3.7 10.3 - - + +
105D GLY 3.2 0.6 - - - -
106D GLU* 1.3 77.7 - - - +
108D ALA* 1.3 57.8 + - - +
110D HIS* 3.4 2.6 + - + +
111D ALA* 2.9 30.1 + - - +
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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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99D VAL* 4.5 10.0 - - + +
100D ARG* 4.8 14.8 - - + -
103D LEU* 3.9 30.4 - - + +
104D PRO 3.5 3.8 + - - +
105D GLY* 2.9 11.5 + - - +
107D LEU* 1.3 77.7 - - - +
109D LYS* 1.3 65.2 + - + +
111D ALA* 3.3 6.4 + - - +
112D VAL* 2.9 29.7 + - - +
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Residues in contact with LYS 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 GLY* 3.0 18.1 + - - +
106D GLU* 3.1 38.9 + - - +
108D ALA* 1.3 77.8 - - + +
110D HIS* 1.3 67.8 + - + +
112D VAL* 3.3 4.7 + - - +
113D SER* 3.0 23.3 + - - -
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Residues in contact with HIS 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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58C TYR* 3.0 39.0 - + + +
62C GLU* 5.6 0.4 - - - -
106D GLU* 3.0 39.4 + - + +
107D LEU* 4.9 0.4 - - + -
109D LYS* 1.3 79.8 - - + +
111D ALA* 1.3 63.0 + - - +
113D SER* 3.3 8.0 + - - -
114D GLU* 2.9 31.1 + - + +
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Residues in contact with ALA 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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51C TYR* 4.2 0.4 - - - -
55C VAL* 3.7 41.7 - - + +
58C TYR* 4.2 12.4 - - + -
99D VAL* 4.0 13.9 - - + -
103D LEU* 4.8 4.3 - - + -
107D LEU 2.9 18.5 + - - +
108D ALA* 3.6 4.5 - - - +
109D LYS 3.3 0.2 - - - -
110D HIS* 1.3 77.2 - - - +
112D VAL* 1.3 57.3 + - - +
114D GLU* 3.3 4.3 + - - +
115D GLY* 2.9 24.9 + - - -
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Residues in contact with VAL 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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51C TYR* 3.2 17.3 + - + +
96D GLN* 3.4 34.8 - - + +
99D VAL* 4.8 6.3 - - + -
100D ARG* 4.2 32.1 - - + +
108D ALA 2.9 19.1 + - - +
109D LYS* 3.8 4.9 - - - +
111D ALA* 1.3 76.1 - - - +
113D SER* 1.3 63.6 + - - +
115D GLY 3.3 0.2 + - - -
116D THR* 2.7 35.9 + - - +
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Residues in contact with SER 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 LYS 3.0 17.4 + - - -
110D HIS* 3.5 11.2 - - - -
111D ALA 3.2 0.2 - - - -
112D VAL* 1.3 78.6 - - - +
114D GLU* 1.3 65.3 + - - +
116D THR* 3.4 5.0 + - - -
117D LYS* 3.0 25.5 + - - +
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Residues in contact with GLU 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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24C LEU* 5.9 3.5 - - - +
54C ALA* 4.3 19.6 - - + +
58C TYR* 4.5 29.0 - - + +
110D HIS* 2.9 22.8 + - + +
111D ALA* 3.7 5.2 - - - +
113D SER* 1.3 77.9 + - - +
115D GLY* 1.3 59.2 + - - +
117D LYS* 3.3 27.7 + - - +
118D ALA* 2.9 29.3 + - - +
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Residues in contact with GLY 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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51C TYR* 3.4 41.7 - - - -
54C ALA* 4.6 1.1 - - - +
55C VAL* 5.1 0.2 - - - +
111D ALA 2.9 14.5 + - - -
114D GLU* 1.3 78.5 - - - +
116D THR* 1.3 56.7 + - - +
118D ALA* 3.2 3.4 + - - +
119D VAL* 2.9 33.6 + - - +
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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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51C TYR* 3.6 4.6 - - - -
96D GLN* 3.8 14.0 + - - -
112D VAL* 2.7 27.2 + - - +
113D SER* 3.7 4.9 - - - -
115D GLY* 1.3 75.2 - - - +
117D LYS* 1.3 65.0 + - - +
119D VAL* 3.2 5.6 + - - +
120D THR* 3.0 38.8 + - + +
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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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22C ALA 5.1 8.9 + - - -
23C GLY 5.9 0.8 + - - -
24C LEU* 5.6 6.2 - - - +
113D SER* 3.0 18.8 + - - +
114D GLU* 3.5 28.7 - - - +
116D THR* 1.3 77.6 - - - +
118D ALA* 1.3 59.2 + - - +
120D THR* 2.8 22.3 + - - +
121D LYS* 2.9 28.0 + - + +
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Residues in contact with ALA 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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22C ALA* 4.6 7.8 - - + +
24C LEU* 4.0 19.1 - - + -
50C VAL* 3.5 25.7 - - + +
54C ALA* 4.3 6.3 - - + -
114D GLU 2.9 17.0 + - - +
115D GLY* 3.6 5.6 - - - +
116D THR 3.2 0.2 - - - -
117D LYS* 1.3 79.8 - - - +
119D VAL* 1.3 56.9 + - - +
121D LYS* 3.7 5.8 - - - +
122D TYR* 2.8 31.7 + - - +
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Residues in contact with VAL 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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47C GLY* 4.2 27.6 - - - +
50C VAL* 5.0 2.0 - - + -
51C TYR* 3.9 21.3 - - + +
92D SER* 4.6 10.8 - - - +
115D GLY 2.9 19.6 + - - +
116D THR* 3.2 5.6 + - - +
118D ALA* 1.3 76.4 - - - +
120D THR* 1.3 66.6 + - + +
122D TYR* 3.2 7.9 + - + +
123D THR* 3.0 35.7 + - - +
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Residues in contact with THR 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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116D THR* 3.0 24.2 + - + +
117D LYS* 2.8 25.5 + - - +
119D VAL* 1.3 80.3 - - + +
121D LYS* 1.3 61.4 + - - +
123D THR* 3.5 6.3 + - - -
124D SER* 3.4 18.7 + - - -
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Residues in contact with LYS 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 SER 3.4 6.5 + - - -
21C ARG* 2.6 35.0 + - - +
22C ALA* 3.4 17.0 - - - +
23C GLY* 3.4 17.2 - - - +
117D LYS* 2.9 29.3 + - + +
118D ALA* 3.8 5.6 - - - +
120D THR* 1.3 76.9 + - - +
122D TYR* 1.3 62.8 + - - +
124D SER* 2.5 29.3 + - - +
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Residues in contact with TYR 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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18C ARG* 3.6 49.4 + - + +
21C ARG* 4.2 34.6 + - + +
22C ALA* 5.1 2.2 - - + -
46C ALA* 4.4 30.7 - - + +
47C GLY* 5.2 6.5 - - - -
50C VAL* 4.5 20.4 - - + -
118D ALA 2.8 17.7 + - - +
119D VAL* 3.2 7.2 + - + +
121D LYS* 1.3 78.3 - - - +
123D THR* 1.3 69.8 + - - +
124D SER 3.2 5.0 + - - -
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Residues in contact with THR 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 VAL* 3.0 25.4 + - - +
120D THR* 4.0 7.1 - - - -
121D LYS 3.3 0.2 - - - -
122D TYR* 1.3 83.7 - - - +
124D SER* 1.3 59.9 + - - +
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Residues in contact with SER 124 (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 ARG* 5.9 5.6 - - - -
120D THR 3.4 9.3 + - - -
121D LYS* 2.5 31.1 + - - +
122D TYR 3.1 4.5 - - - -
123D THR* 1.3 82.0 - - - +
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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