Contacts of the helix formed by residues 113 - 134 (chain K) in PDB entry 5FWP
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 113 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108K PRO* 4.7 7.4 - - + -
111K GLY 3.2 7.2 - - - +
112K LEU* 1.4 98.4 - - + +
114K ALA* 1.3 66.8 + - - +
115K GLU* 3.1 4.0 - - + +
116K THR* 3.0 32.4 + - - +
117K ILE* 3.1 10.4 + - - +
263K GLU* 5.7 1.1 - - + -
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Residues in contact with ALA 114 (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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112K LEU 3.0 3.4 + - - -
113K PRO* 1.3 71.4 - - - +
115K GLU* 1.3 54.3 + - + +
117K ILE* 3.2 2.7 + - - +
118K LYS* 2.7 51.0 + - - +
208K PHE* 3.7 18.6 - - + -
263K GLU* 3.6 32.1 + - + +
265K GLU* 5.4 5.4 - - + +
294K TYR* 4.6 2.1 + - - +
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Residues in contact with GLU 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K PRO* 3.1 3.5 - - + +
114K ALA* 1.3 75.6 - - + +
116K THR* 1.3 66.2 + - - +
118K LYS* 2.8 41.3 + - - +
119K ASP* 3.1 21.8 + - - +
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Residues in contact with THR 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K TYR* 3.6 25.1 - - + +
112K LEU* 5.6 0.7 - - + -
113K PRO* 3.0 29.2 + - + +
115K GLU* 1.3 78.5 - - - +
117K ILE* 1.3 59.4 + - + +
119K ASP* 3.2 7.3 + - - +
120K LEU* 3.0 35.7 + - + +
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Residues in contact with ILE 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112K LEU* 3.3 43.1 - - + +
113K PRO 3.1 5.7 + - - +
114K ALA 3.5 6.1 - - - +
116K THR* 1.3 75.2 - - - +
118K LYS* 1.3 54.8 + - - +
120K LEU* 3.5 6.0 - - + -
121K MET* 2.6 48.8 + - + +
204K PHE* 4.6 8.1 - - + +
207K MET* 4.0 17.5 - - + -
208K PHE* 3.4 59.5 - - + +
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Residues in contact with LYS 118 (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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114K ALA* 2.7 30.1 + - - +
115K GLU* 2.8 43.7 + - - +
116K THR 3.3 0.2 - - - -
117K ILE* 1.3 72.0 - - - +
119K ASP* 1.3 63.3 + - - +
121K MET* 4.2 0.7 - - - -
122K ARG* 3.0 26.7 + - - +
265K GLU* 2.9 29.5 + - - -
294K TYR* 3.1 52.8 + - + +
295K LEU* 3.2 24.6 - - + +
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Residues in contact with ASP 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K GLU 3.1 10.3 + - - +
116K THR* 3.5 9.6 - - - +
117K ILE 3.2 0.4 - - - -
118K LYS* 1.3 79.3 - - - +
120K LEU* 1.3 58.1 + - - +
122K ARG* 3.1 42.2 + - - +
123K GLN* 2.8 50.4 + - - +
152K GLY* 3.7 19.2 - - - +
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Residues in contact with LEU 120 (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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103K TYR* 3.7 29.6 - - + +
116K THR* 3.0 28.8 + - + +
117K ILE 3.7 3.4 - - - +
119K ASP* 1.3 78.0 - - - +
121K MET* 1.3 56.6 + - - +
123K GLN* 3.3 1.0 + - - -
124K PHE* 2.9 26.7 + - - +
148K VAL* 4.0 15.5 - - + -
152K GLY* 3.2 33.4 - - - +
154K VAL* 3.3 28.7 - - + +
204K PHE* 4.5 2.6 - - - -
207K MET* 3.4 31.4 - - + -
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Residues in contact with MET 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K ILE* 2.6 34.3 + - + +
118K LYS 3.5 5.4 - - - +
120K LEU* 1.3 73.0 - - - +
122K ARG* 1.3 57.4 + - - +
124K PHE* 3.2 2.8 + - - +
125K LEU* 2.8 45.9 + - + +
204K PHE* 3.6 54.9 - - + -
208K PHE* 4.9 3.6 - - + -
264K MET* 5.7 3.4 - - + -
268K GLY 5.9 2.2 - - - +
271K LEU* 5.0 7.2 - - - -
272K LEU* 6.5 1.1 - - + -
275K MET* 5.0 9.6 - - + -
289K ALA* 6.2 0.4 - - - -
294K TYR* 3.6 25.4 - - + +
295K LEU* 3.6 21.3 - - + -
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Residues in contact with ARG 122 (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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312A TRP* 5.9 6.4 - - - -
118K LYS* 3.0 16.2 + - - +
119K ASP* 3.1 45.0 + - - +
121K MET* 1.3 74.7 - - - +
123K GLN* 1.3 60.0 + - - +
126K ARG* 2.9 47.9 + - - +
290K LEU* 3.3 24.5 - - + +
295K LEU* 2.9 45.7 + - + -
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Residues in contact with GLN 123 (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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21E PRO* 6.0 0.2 - - - +
22E ASN* 2.8 54.4 + - - +
119K ASP* 2.8 47.2 + - - +
120K LEU* 3.5 6.3 - - - +
122K ARG* 1.3 77.4 - - - +
124K PHE* 1.3 61.3 + - - +
126K ARG* 3.1 24.3 + - - +
127K GLY 3.1 8.7 + - - -
152K GLY 3.8 21.1 - - - +
153K THR* 4.2 10.2 + - - +
154K VAL* 3.6 13.0 - - + +
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Residues in contact with PHE 124 (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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22E ASN* 5.5 0.2 - - - -
120K LEU 2.9 17.7 + - - +
121K MET 3.4 4.5 - - - +
123K GLN* 1.3 77.4 - - - +
125K LEU* 1.3 61.4 + - + +
127K GLY* 3.1 4.7 + - - -
128K LEU* 2.9 50.9 + - + +
141K LEU* 3.8 20.2 - - + -
146K ILE* 3.6 23.6 - - + -
154K VAL* 3.9 16.1 - - + +
156K LEU* 3.4 35.1 - - + +
196K ASP* 4.1 5.2 - - - -
200K VAL* 3.5 41.7 - - + -
204K PHE* 3.9 12.8 - + + -
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Residues in contact with LEU 125 (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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121K MET* 2.8 30.1 + - + +
124K PHE* 1.3 77.0 - - + +
126K ARG* 1.3 60.2 + - - +
128K LEU* 3.0 27.2 + - + +
129K ASP* 2.9 31.4 + - - +
197K MET* 3.9 22.7 - - + -
204K PHE* 4.9 7.2 - - + -
275K MET* 5.1 2.7 - - - -
286K ALA* 3.8 12.0 - - - +
289K ALA* 3.7 10.1 - - + -
290K LEU* 3.6 32.8 - - + +
295K LEU* 3.6 22.7 - - + -
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Residues in contact with ARG 126 (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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310A ASN* 5.9 3.0 - - - +
20E HIS* 3.7 21.5 + - + +
21E PRO* 6.2 0.9 - - - -
22E ASN* 3.1 23.9 + - - +
122K ARG* 2.9 46.9 + - - +
123K GLN* 3.1 31.7 + - - +
125K LEU* 1.3 75.6 - - - +
127K GLY* 1.3 62.7 + - - +
129K ASP* 3.2 13.4 + - + +
130K PHE 3.3 9.2 + - - -
290K LEU* 3.7 25.1 - - + +
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Residues in contact with GLY 127 (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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20E HIS* 3.8 6.3 - - - -
22E ASN* 3.7 21.9 - - - +
23E ILE* 3.6 14.4 - - - +
123K GLN 3.1 5.1 + - - -
124K PHE 3.1 8.7 + - - -
126K ARG* 1.3 78.5 - - - +
128K LEU* 1.3 61.7 + - - +
130K PHE* 3.2 5.7 + - - +
131K LEU* 3.0 26.1 + - - +
156K LEU* 4.4 1.6 - - - -
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Residues in contact with LEU 128 (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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124K PHE* 2.9 45.0 + - + +
125K LEU* 3.0 19.9 + - + +
127K GLY* 1.3 74.4 - - - +
129K ASP* 1.3 55.0 + - - +
131K LEU* 2.9 19.0 + - + +
132K HIS* 2.6 52.2 + - + +
138K HIS* 4.3 0.9 - - - +
156K LEU* 4.2 3.1 - - + -
196K ASP* 3.1 32.3 - - - +
197K MET* 3.7 16.6 - - + -
286K ALA* 3.6 20.0 - - + -
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Residues in contact with ASP 129 (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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125K LEU 2.9 13.7 + - - -
126K ARG* 3.2 8.7 + - + +
128K LEU* 1.3 75.3 - - - +
130K PHE* 1.3 57.9 - - - +
132K HIS* 3.8 7.0 - - - +
133K ALA* 2.9 30.4 + - - +
286K ALA* 3.3 7.3 - - - +
287K PHE* 3.0 47.8 + - - +
290K LEU* 3.2 25.7 - - + +
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Residues in contact with PHE 130 (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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18E GLU* 3.8 17.3 - - + -
19E THR* 3.5 29.8 - - - -
20E HIS* 3.5 42.6 - + + +
23E ILE* 3.7 12.1 - - + -
28E LEU* 3.8 22.9 - - + -
32E ARG* 4.2 3.1 - - - -
126K ARG 3.3 2.4 + - - -
127K GLY 3.2 8.5 + - - +
128K LEU 3.2 0.2 - - - -
129K ASP* 1.3 78.7 - - - +
131K LEU* 1.3 62.8 + - + +
133K ALA* 3.2 6.6 + - + +
134K ASN* 2.7 62.6 + - + -
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Residues in contact with LEU 131 (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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23E ILE* 3.5 33.4 - - + -
28E LEU* 4.2 3.8 - - + -
127K GLY 3.0 13.8 + - - +
128K LEU* 2.9 12.0 + - + +
130K PHE* 1.3 80.5 - - + +
132K HIS* 1.3 60.6 + - - +
135K CYS 2.9 6.8 + - - -
136K ILE* 2.7 58.1 + - + +
138K HIS* 3.7 25.8 - - + +
156K LEU* 3.7 20.2 - - + -
159K PHE* 3.7 23.1 - - + -
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Residues in contact with HIS 132 (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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128K LEU* 2.6 48.8 + - + +
129K ASP* 3.8 7.0 - - - +
131K LEU* 1.3 71.5 - - - +
133K ALA* 1.3 65.4 + - - +
135K CYS* 3.0 20.8 + - - +
136K ILE 4.8 0.6 + - - +
138K HIS* 5.4 0.2 - + - -
191K TYR* 3.2 31.1 + + - -
193K THR* 3.5 47.7 + - + +
196K ASP* 4.0 7.4 - - + -
286K ALA* 3.8 13.9 - - + +
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Residues in contact with ALA 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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196A ARG* 5.1 20.6 - - - +
129K ASP 2.9 17.7 + - - +
130K PHE* 3.2 9.8 + - + +
132K HIS* 1.3 77.4 - - - +
134K ASN* 1.3 62.6 + - - +
135K CYS* 3.6 5.9 + - - -
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Residues in contact with ASN 134 (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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18E GLU* 5.3 3.3 - - - +
31E TRP* 4.1 5.9 - - - -
32E ARG* 4.1 18.5 + - - +
130K PHE* 2.7 63.6 + - + +
132K HIS 3.2 0.2 - - - -
133K ALA* 1.3 82.1 - - - +
135K CYS* 1.3 71.1 + - - +
136K ILE* 3.3 26.8 + - + +
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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