Contacts of the helix formed by residues 107 - 124 (chain D) in PDB entry 5GOU
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 GLU 107 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.3 6.9 - - - +
29D TYR* 4.3 15.1 - - - -
30D ALA* 3.9 16.7 - - + +
34D TYR* 4.9 7.5 + - - +
62D GLU* 6.1 3.1 - - - +
103D ALA 4.2 1.8 + - - -
104D LEU 4.0 1.4 + - - -
106D LEU* 1.3 121.3 - - + +
108D LYS* 1.3 52.0 + - - +
109D ASN* 2.9 10.4 - - - +
110D VAL* 2.8 57.1 + - + +
111D ASN* 2.4 37.3 + - - -
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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
----------------------------------------------------------
104D LEU* 3.2 43.6 + - + +
105D HIS* 4.0 9.6 + - + +
106D LEU 3.7 0.6 - - - -
107D GLU* 1.3 75.5 - - - +
109D ASN* 1.3 59.2 + - - +
111D ASN* 4.0 12.1 - - - +
112D GLN* 3.5 19.1 + - - +
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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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26D LEU* 6.0 0.2 - - - -
105D HIS 4.3 9.2 + - - +
106D LEU 3.7 7.6 + - - +
107D GLU* 2.9 11.2 - - - +
108D LYS* 1.3 80.2 - - - +
110D VAL* 1.3 54.0 + - - +
111D ASN 3.4 0.4 - - - -
112D GLN* 3.4 15.4 + - - +
113D SER* 2.6 32.7 + - - -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN* 3.7 15.7 - - - +
26D LEU* 3.4 37.5 - - + +
27D GLU* 4.0 15.3 - - - +
30D ALA* 5.6 0.4 - - + -
62D GLU* 5.4 2.0 - - - +
107D GLU* 2.8 49.7 + - + +
109D ASN* 1.3 71.2 - - - +
111D ASN* 1.3 59.3 + - - +
113D SER* 3.5 3.6 - - - -
114D LEU* 2.2 52.8 + - + +
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Residues in contact with ASN 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 GLU* 2.4 32.6 + - - +
108D LYS* 4.0 11.9 - - - +
110D VAL* 1.3 77.6 - - - +
112D GLN* 1.3 56.7 + - - +
114D LEU* 3.3 21.3 + - - +
115D LEU* 2.9 35.5 + - + +
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Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS 3.5 13.9 + - - +
109D ASN* 3.4 18.9 + - - +
110D VAL 3.1 0.2 - - - -
111D ASN* 1.3 76.8 - - - +
113D SER* 1.3 60.9 + - - +
115D LEU* 2.9 13.0 + - + +
116D GLU* 2.8 54.7 + - + +
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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
----------------------------------------------------------
23D GLN* 2.9 20.1 + - - -
26D LEU* 3.5 18.7 - - - +
109D ASN 2.6 22.2 + - - -
110D VAL* 2.7 13.8 + - - -
112D GLN* 1.3 71.0 - - - +
114D LEU* 1.3 59.7 + - - -
116D GLU* 3.6 14.3 + - - +
117D LEU* 3.2 28.4 + - - +
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Residues in contact with LEU 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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23D GLN* 4.0 17.3 - - + +
27D GLU* 4.0 18.2 - - - +
65D HIS* 6.0 6.3 - - + +
69D LEU* 5.8 4.3 - - + -
110D VAL* 2.2 45.2 + - + +
111D ASN* 3.4 22.7 - - - +
113D SER* 1.3 69.5 - - - +
115D LEU* 1.3 61.9 + - + +
117D LEU* 3.4 9.9 - - + +
118D HIS* 3.3 16.1 + - - +
133D ILE* 3.9 26.3 - - + +
135D THR* 6.4 2.7 - - + -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ASN* 2.9 21.3 + - + +
112D GLN* 2.9 15.8 + - + +
114D LEU* 1.3 75.5 - - + +
116D GLU* 1.3 60.0 + - + +
117D LEU 3.1 1.3 - - - -
118D HIS* 3.1 16.9 + - + +
119D LYS* 2.9 27.5 + - - +
133D ILE* 6.2 2.0 - - + -
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D GLN* 2.8 44.0 + - + +
113D SER* 4.0 14.1 - - - +
114D LEU 3.4 0.2 - - - -
115D LEU* 1.3 71.7 - - + +
117D LEU* 1.3 61.9 + - + +
119D LYS* 3.5 10.7 + - + +
120D LEU* 2.8 27.8 + - - +
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Residues in contact with LEU 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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16D SER 5.2 0.2 - - - +
19D ALA* 3.6 42.8 - - + +
20D ILE* 4.3 15.5 - - + -
22D ARG* 6.0 1.1 - - - +
23D GLN* 3.7 22.2 - - + +
113D SER* 3.2 24.6 + - - +
114D LEU* 3.4 14.1 - - + +
115D LEU 3.1 0.4 - - - -
116D GLU* 1.3 79.0 - - + +
118D HIS* 1.3 51.8 + - - +
120D LEU* 3.1 18.9 + - + +
121D ALA* 2.7 35.9 + - - +
129D LEU* 4.8 6.2 - - + +
133D ILE* 3.8 12.3 - - + +
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Residues in contact with HIS 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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114D LEU 3.3 6.7 + - - +
115D LEU* 3.1 21.6 + - + +
117D LEU* 1.3 78.5 - - - +
119D LYS* 1.3 53.6 + - - +
121D ALA* 3.5 1.7 + - - -
122D THR* 2.7 43.5 + - - -
130D CYS* 3.6 43.0 + - + -
133D ILE* 3.5 27.7 - - + +
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Residues in contact with LYS 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 LEU 2.9 15.6 + - - +
116D GLU* 3.8 10.5 - - + +
118D HIS* 1.3 75.4 - - - +
120D LEU* 1.3 60.5 + - - +
122D THR* 4.0 6.0 - - - -
123D ASP* 2.9 45.1 + - - +
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Residues in contact with LEU 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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15D ASP* 3.6 26.2 - - + +
16D SER* 3.5 30.7 - - - +
19D ALA* 3.8 11.7 - - + -
22D ARG* 5.4 2.9 - - - +
116D GLU 2.8 18.7 + - - +
117D LEU* 3.1 25.3 + - + +
119D LYS* 1.3 75.0 - - - +
121D ALA* 1.3 69.0 + - - +
123D ASP* 3.3 6.3 + - - +
124D LYS* 3.2 32.9 + - + +
129D LEU* 4.3 4.5 - - + -
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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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16D SER* 5.5 0.2 - - - -
117D LEU 2.7 19.8 + - - +
118D HIS* 4.0 2.2 - - - +
120D LEU* 1.3 76.9 - - - +
122D THR* 1.3 61.3 + - - +
124D LYS* 3.5 2.0 + - - +
125D ASN 3.2 3.5 + - - -
126D ASP* 2.9 35.4 + - + +
129D LEU* 3.7 34.3 - - + -
130D CYS* 3.5 23.0 - - - +
133D ILE* 5.2 0.2 - - + -
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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 HIS* 2.7 36.1 + - - -
119D LYS* 4.0 7.3 - - - -
120D LEU 3.2 0.2 - - - -
121D ALA* 1.3 77.6 - - - +
123D ASP* 1.3 66.2 + - - +
125D ASN* 3.2 20.0 + - - +
126D ASP 5.2 0.4 - - - +
130D CYS* 3.6 9.0 - - - -
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Residues in contact with ASP 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 LYS* 2.9 35.5 + - - +
120D LEU* 3.3 7.1 + - - +
122D THR* 1.3 81.3 - - - +
124D LYS* 1.3 71.8 + - + +
125D ASN* 3.4 3.9 + - - +
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Residues in contact with LYS 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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11D ASN* 4.4 7.8 + - - +
13D HIS* 3.4 49.7 + - + +
15D ASP* 6.1 1.3 - - + -
16D SER* 3.9 20.6 - - - +
120D LEU* 3.2 21.8 + - + +
121D ALA* 3.5 3.8 + - - +
122D THR 3.2 0.8 - - - -
123D ASP* 1.3 88.2 + - + +
125D ASN* 1.3 72.1 + - - +
126D ASP* 3.3 6.5 + - + +
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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
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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