Contacts of the helix formed by residues 130 - 143 (chain K) in PDB entry 5G04
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 SER 130 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16J GLN* 4.7 0.2 + - - -
127K SER* 3.7 16.6 + - - -
128K ILE 2.6 4.4 + - - -
129K LYS* 1.3 73.9 - - - +
131K SER* 1.3 74.2 + - - -
132K ILE 3.2 0.9 - - - -
133K CYS* 2.9 18.6 + - - +
134K LEU* 2.9 10.3 + - - -
156K ALA* 3.7 13.5 - - - +
159K LEU* 3.7 24.7 - - - -
160K ASP* 3.5 34.8 + - - +
163K CYS* 5.9 1.7 - - - -
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Residues in contact with SER 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J GLN* 2.7 31.0 + - - +
18J GLN* 3.2 28.4 - - - +
74K TYR* 4.2 7.3 - - - -
128K ILE* 2.7 30.3 + - - +
130K SER* 1.3 76.7 + - - +
132K ILE* 1.3 56.6 + - - -
134K LEU* 3.0 14.8 + - - +
135K LEU* 2.9 26.3 + - - +
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Residues in contact with ILE 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K GLU* 4.4 13.5 - - + +
73K ARG* 4.1 31.4 - - + +
74K TYR* 3.9 42.3 - - + +
93K LEU* 3.6 25.9 - - + +
128K ILE* 2.9 18.2 + - + +
129K LYS* 3.5 20.9 - - - +
131K SER* 1.3 78.2 + - - +
133K CYS* 1.3 66.7 + - - +
135K LEU* 3.3 1.6 + - - +
136K ARG* 3.2 24.4 + - - +
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Residues in contact with CYS 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K LYS 2.1 35.9 - - - -
130K SER* 2.9 8.0 + - - +
132K ILE* 1.3 77.9 - - - +
134K LEU* 1.3 64.7 + - - +
136K ARG* 3.3 20.1 + - - +
137K GLY 3.3 3.5 + - - -
152K SER* 2.7 30.4 + - - +
155K GLU* 4.7 6.1 - - + -
156K ALA* 4.1 19.1 - - + +
159K LEU* 4.0 12.3 - - - -
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Residues in contact with LEU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J GLN* 3.2 33.2 - - - +
74K TYR* 6.0 0.7 - - - +
78K ARG* 5.9 2.2 - - - +
130K SER 2.9 10.2 + - - +
131K SER* 3.0 10.1 + - - +
133K CYS* 1.3 75.9 - - - +
135K LEU* 1.3 71.1 + - + +
137K GLY* 3.0 4.0 + - - -
138K LYS* 2.9 45.4 + - + +
152K SER 4.9 0.2 - - - -
153K TYR* 3.9 11.5 - - + -
156K ALA* 3.7 15.2 - - + +
163K CYS* 4.0 18.6 - - - -
165K GLU* 3.8 22.2 - - + +
166K ALA* 4.2 9.9 - - + +
169K LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K TYR* 3.7 19.3 - - + +
77K ALA* 3.8 16.6 - - + -
78K ARG* 3.7 44.2 - - + +
81K TYR* 4.0 29.2 - - + -
93K LEU* 4.7 3.4 - - + -
131K SER 2.9 12.0 + - - +
132K ILE 3.7 8.3 - - - +
133K CYS 3.3 0.2 - - - -
134K LEU* 1.3 80.9 - - + +
136K ARG* 1.3 67.6 + - - +
138K LYS* 2.9 20.7 + - + +
139K ILE* 3.0 28.1 + - + +
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Residues in contact with ARG 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K LEU* 4.1 14.4 - - + +
93K LEU* 3.6 41.9 + - + +
132K ILE* 3.2 16.5 + - - +
133K CYS* 3.4 32.6 + - - +
134K LEU 3.2 0.2 - - - -
135K LEU* 1.3 74.6 - - - +
137K GLY* 1.3 63.0 + - - +
139K ILE* 3.1 11.2 + - - +
140K TYR* 3.1 55.4 + - + -
152K SER* 3.5 10.8 + - - +
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Residues in contact with GLY 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K CYS 3.3 0.4 + - - -
134K LEU 3.0 8.0 + - - -
136K ARG* 1.3 79.0 - - - +
138K LYS* 1.3 61.9 + - - +
140K TYR* 3.1 10.5 + - - -
141K ASP 3.1 9.9 + - - -
149K ALA* 3.5 19.1 - - - +
152K SER* 3.1 26.3 + - - -
153K TYR* 3.6 14.0 + - - -
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Residues in contact with LYS 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLN* 5.6 4.2 - - - +
78K ARG* 5.8 7.1 - - - +
81K TYR* 3.7 42.4 + - + +
134K LEU* 2.9 31.1 + - + +
135K LEU* 2.9 17.0 + - + +
137K GLY* 1.3 74.4 - - - +
139K ILE* 1.3 61.9 + - - +
141K ASP* 3.3 6.8 + - - +
142K ALA* 3.3 18.2 + - - +
153K TYR* 3.4 16.5 + - + +
165K GLU* 3.9 22.9 + - - -
169K LEU* 4.2 15.6 - - + +
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Residues in contact with ILE 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K TYR* 3.8 21.8 - - + -
86K HIS* 4.3 15.9 - - + +
87K GLN 4.4 11.2 - - - +
89K ALA* 3.8 24.9 - - + +
90K LEU* 4.3 32.5 - - + +
93K LEU* 4.6 5.6 - - + -
135K LEU* 3.0 37.1 + - + +
136K ARG* 3.1 9.6 + - - +
138K LYS* 1.3 74.3 - - - +
140K TYR* 1.3 60.6 + - - +
142K ALA* 2.8 9.9 + - - +
143K LEU* 2.8 28.6 + - + +
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Residues in contact with TYR 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K LEU* 3.4 39.9 - - + +
136K ARG* 3.1 49.2 + - + -
137K GLY* 3.1 1.8 + - - +
139K ILE* 1.3 77.2 - - - +
141K ASP* 1.3 56.4 + - - +
143K LEU* 3.4 8.5 + - + -
144K ASP 3.0 5.5 + - - -
145K ASN* 2.8 52.3 + - + +
148K LEU* 4.1 42.5 - - + +
149K ALA* 3.5 22.2 - - + -
152K SER* 4.5 2.7 - - - -
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Residues in contact with ASP 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K GLY 3.1 6.1 + - - +
138K LYS* 3.4 10.8 - - - +
139K ILE 3.1 0.4 - - - -
140K TYR* 1.3 77.1 - - - +
142K ALA* 1.3 58.6 + - - +
144K ASP* 3.0 23.0 + - - +
145K ASN 5.2 0.7 - - - -
146K ARG* 3.8 15.7 - - - +
149K ALA* 3.7 8.1 - - - +
153K TYR* 2.9 38.4 + - - +
169K LEU* 4.0 9.3 - - - +
332K THR* 3.5 32.0 - - + +
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Residues in contact with ALA 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K TYR* 4.5 4.3 - - + +
86K HIS* 3.6 41.5 - - + +
138K LYS 3.3 7.9 + - - +
139K ILE* 2.8 9.9 + - - +
141K ASP* 1.3 77.3 - - - +
143K LEU* 1.3 61.7 + - - +
144K ASP* 3.1 3.7 + - - +
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Residues in contact with LEU 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K HIS* 3.8 28.9 - - + -
87K GLN* 4.2 26.2 - - + +
90K LEU* 4.1 25.1 - - + -
139K ILE* 2.8 16.1 + - + +
140K TYR* 3.8 15.0 - - + +
142K ALA* 1.3 75.7 - - - +
144K ASP* 1.3 65.3 + - - +
145K ASN* 3.2 16.6 + - + +
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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