Contacts of the helix formed by residues 145 - 162 (chain D) in PDB entry 5FLZ
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 GLY 145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA* 3.8 22.0 - - - -
103D ASN* 3.9 10.2 - - - +
104D SER 3.7 29.1 - - - +
105D TRP* 4.3 0.2 - - - -
108D GLY* 4.1 4.2 - - - -
144D GLY* 1.3 74.2 - - - +
146D THR* 1.4 56.3 + - - +
148D SER* 4.1 0.5 - - - -
149D GLY* 3.1 24.4 + - - -
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Residues in contact with THR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA* 5.0 2.1 - - - +
11D GLY* 4.1 24.9 - - - +
70D ASP* 4.4 16.0 + - - +
71D SER 5.8 0.2 - - - +
93D TRP* 6.2 0.4 - - + -
101D ALA* 4.0 12.8 - - - +
108D GLY* 5.4 2.9 - - - -
111D ILE* 6.2 4.5 - - + -
145D GLY* 1.4 68.9 - - - +
147D GLY* 1.4 67.6 + - - +
148D SER 3.2 2.5 + - - -
150D LEU* 3.3 43.3 + - + +
151D GLY 4.1 1.4 + - - -
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Residues in contact with GLY 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA* 4.8 1.2 - - - +
11D GLY* 4.4 15.0 - - - -
140D HIS* 2.9 28.9 + - - +
141D SER* 3.0 26.5 - - - -
144D GLY* 4.4 4.3 - - - -
145D GLY 3.5 2.2 - - - +
146D THR* 1.4 80.4 - - - +
148D SER* 1.3 59.9 + - - +
151D GLY* 4.3 5.2 + - - -
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 3.7 20.2 - - - -
140D HIS* 4.8 3.8 + - - -
141D SER 3.3 3.8 + - - -
142D VAL* 3.9 3.6 - - - +
143D ALA* 3.1 22.2 + - - -
144D GLY 2.8 26.8 + - - -
145D GLY 4.0 1.1 + - - -
146D THR 3.2 0.2 - - - -
147D GLY* 1.3 79.6 - - - +
149D GLY* 1.4 60.6 + - - +
151D GLY 4.3 0.2 - - - -
152D SER* 3.0 29.6 + - - -
186D ASN* 4.0 6.8 - - - +
190D ALA* 4.4 9.4 - - - +
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 3.3 33.0 - - - -
108D GLY 4.0 0.2 - - - -
109D TYR* 3.3 22.9 - - - -
145D GLY 3.1 11.0 + - - -
148D SER* 1.4 76.1 - - - +
150D LEU* 1.4 64.2 + - - +
152D SER 3.5 1.0 + - - -
153D ASN 3.1 17.3 + - - -
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Residues in contact with LEU 150 (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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10D ALA* 5.4 4.9 - - + -
69D MET* 3.8 28.3 - - + -
93D TRP* 4.0 20.2 - - + -
108D GLY* 3.6 15.5 + - - +
111D ILE* 5.4 5.2 - - + -
112D GLY* 3.4 30.5 - - - +
119D ILE* 4.5 11.7 - - + -
146D THR* 3.3 30.8 + - + +
149D GLY* 1.4 73.7 - - - +
151D GLY* 1.4 55.7 + - - +
153D ASN* 3.3 7.7 + - - +
154D LEU* 3.2 42.5 + - + +
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Residues in contact with GLY 151 (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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10D ALA* 4.8 4.9 - - - +
138D LEU* 3.9 27.6 - - - +
140D HIS* 4.8 2.7 - - - -
146D THR 4.1 4.8 + - - -
147D GLY 4.3 7.8 + - - -
148D SER 4.0 3.6 + - - -
149D GLY 3.4 0.4 - - - -
150D LEU* 1.4 71.1 - - - +
152D SER* 1.3 63.7 + - - +
153D ASN 3.3 0.2 - - - -
154D LEU* 3.4 12.0 + - - +
155D LEU* 3.0 24.7 + - - +
194D LEU* 5.6 0.7 - - - -
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Residues in contact with SER 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 3.5 25.1 + - - -
109D TYR* 3.7 9.2 - - - -
140D HIS* 5.3 0.4 - - - -
148D SER 3.0 18.0 + - - -
149D GLY 3.8 1.6 - - - -
150D LEU 3.4 0.2 - - - -
151D GLY* 1.3 76.6 - - - +
153D ASN* 1.4 62.2 + - - +
155D LEU* 3.4 4.2 + - - +
156D GLU* 3.4 23.0 + - - +
190D ALA* 3.6 17.0 + - - +
193D ARG* 3.8 19.8 - - - +
194D LEU* 4.2 9.0 - - - +
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Residues in contact with ASN 153 (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 TYR* 3.3 45.0 + - + +
112D GLY* 3.4 27.3 + - - -
113D THR* 3.3 20.9 + - - +
116D GLN* 5.8 2.2 - - - +
149D GLY 3.1 13.8 + - - +
150D LEU* 3.3 10.3 + - - +
152D SER* 1.4 76.3 - - - +
154D LEU* 1.3 73.0 + - - +
156D GLU* 3.6 2.6 + - - +
157D ALA* 3.3 22.5 + - - +
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.5 17.3 - - + -
69D MET* 3.3 36.8 - - + -
112D GLY 6.1 0.2 - - - +
119D ILE* 3.9 25.8 - - + -
120D LEU* 5.9 4.0 - - + -
123D ILE* 4.4 14.1 - - + -
138D LEU* 5.6 1.6 - - + -
150D LEU* 3.2 32.2 + - + +
151D GLY* 3.7 11.4 - - - +
153D ASN* 1.3 83.4 - - - +
155D LEU* 1.3 58.2 + - - +
157D ALA* 3.3 6.3 + - + +
158D LEU* 2.9 39.5 + - + +
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 5.3 2.5 - - + -
136D PHE* 6.1 2.9 - - + -
138D LEU* 4.1 28.9 - - + -
151D GLY 3.0 15.7 + - - +
152D SER* 3.9 7.9 - - - +
153D ASN 3.2 0.4 - - - -
154D LEU* 1.3 78.0 - - - +
156D GLU* 1.4 54.9 + - - +
158D LEU* 3.4 9.0 + - + -
159D CYS* 3.1 27.7 + - - +
167D LEU* 3.6 27.9 - - + +
168D THR 5.3 2.0 - - - +
169D THR* 5.1 3.6 - - - -
193D ARG* 4.4 7.2 - - + +
194D LEU* 4.4 15.5 - - + -
197D ASP* 3.9 9.9 - - + -
198D SER* 3.7 39.7 - - - +
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D TYR* 3.9 17.8 + - - +
152D SER 3.4 13.0 + - - +
153D ASN 4.1 1.8 - - - +
155D LEU* 1.4 74.5 - - - +
157D ALA* 1.3 65.6 + - - +
159D CYS* 3.4 5.7 + - - +
160D ASP* 2.9 58.2 - - - +
193D ARG* 4.4 11.4 - - + +
197D ASP* 3.4 29.5 - - - +
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Residues in contact with ALA 157 (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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120D LEU* 5.3 9.6 - - + -
153D ASN* 3.3 13.8 + - - +
154D LEU* 3.3 12.4 + - + +
156D GLU* 1.3 80.4 + - - +
158D LEU* 1.3 67.5 + - + +
160D ASP* 3.4 7.1 + - - +
161D ARG* 2.9 25.7 + - - +
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Residues in contact with LEU 158 (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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8D LEU* 3.7 26.9 - - + -
120D LEU* 4.8 12.1 - - + -
123D ILE* 4.0 26.0 - - + -
136D PHE* 3.7 42.2 - - + -
154D LEU* 2.9 25.5 + - + +
155D LEU* 3.8 8.5 - - + +
157D ALA* 1.3 81.9 - - + +
159D CYS* 1.4 55.0 + - - +
161D ARG* 4.5 4.9 - - + +
162D TYR* 2.9 43.6 + - + +
167D LEU* 3.9 14.3 - - + +
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Residues in contact with CYS 159 (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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155D LEU 3.1 12.0 + - - +
156D GLU 3.6 2.9 - - - +
157D ALA 3.2 0.2 - - - -
158D LEU* 1.4 77.0 - - - +
160D ASP* 1.3 63.3 + - - +
162D TYR 3.5 12.3 - - - +
163D PRO* 3.7 13.5 - - - +
167D LEU* 4.1 13.2 - - + +
196D GLU 5.1 2.2 - - - -
197D ASP* 3.1 43.5 - - + +
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Residues in contact with ASP 160 (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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156D GLU* 2.9 41.4 + - - +
157D ALA* 3.8 8.0 - - - +
159D CYS* 1.3 80.3 - - - +
161D ARG* 1.4 63.8 + - - +
163D PRO* 3.9 10.6 - - - +
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Residues in contact with ARG 161 (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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120D LEU* 3.4 41.6 - - - +
124D ASP* 3.0 40.5 + - - -
157D ALA 2.9 17.9 + - - +
158D LEU* 4.1 2.7 - - + +
160D ASP* 1.4 75.8 - - - +
162D TYR* 1.3 101.5 + - + +
163D PRO* 3.4 7.4 - - - +
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Residues in contact with TYR 162 (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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123D ILE* 5.5 1.6 - - + -
124D ASP* 3.7 14.5 + - - +
127D ILE* 3.6 41.4 - - + +
133D PHE* 6.3 0.7 - + + -
136D PHE* 4.6 17.1 - + + -
158D LEU* 2.9 27.3 + - + +
159D CYS* 3.5 4.5 - - - +
161D ARG* 1.3 122.9 + - + +
163D PRO* 1.3 62.7 - - - +
164D LYS* 3.4 2.9 + - + -
165D LYS* 4.1 31.5 + - + +
167D LEU* 4.6 9.7 - - - +
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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