Contacts of the helix formed by residues 148 - 160 (chain D) in PDB entry 5CYP
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 ARG 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C SER* 5.8 3.6 - - - +
93C ASP* 3.6 27.4 - - + +
31D GLN* 5.7 4.5 - - - +
141D PRO* 6.6 0.2 - - + -
146D SER 3.5 3.3 + - - +
147D LEU* 1.3 77.0 - - - +
149D PRO* 1.3 74.1 - - + +
150D LEU* 2.9 6.3 + - + +
151D ASP* 3.1 23.7 + - - +
152D ILE* 3.1 11.3 + - - +
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Residues in contact with PRO 149 (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 ASP* 3.6 17.9 - - + +
94C HIS* 3.7 36.1 - - + +
95C ILE 5.7 0.4 - - - +
147D LEU 4.2 3.1 - - - +
148D ARG* 1.3 87.1 - - + +
150D LEU* 1.3 60.1 + - - +
152D ILE* 3.8 13.7 - - + +
153D GLU* 3.1 25.6 + - - +
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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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92C GLY 4.5 7.4 - - - +
93C ASP* 2.9 21.3 + - - +
94C HIS* 4.4 13.0 - - - +
95C ILE* 5.0 5.2 - - + +
31D GLN* 3.7 21.5 - - - +
91D PHE* 4.0 19.7 - - + -
92D GLY* 3.6 28.5 - - - -
97D ASN* 4.0 24.9 - - + +
148D ARG* 2.9 3.8 + - + +
149D PRO* 1.3 76.0 - - - +
151D ASP* 1.3 63.5 + - - +
153D GLU* 3.9 3.1 - - + +
154D PHE* 3.0 38.4 + - + +
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Residues in contact with ASP 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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31D GLN* 4.2 14.0 + - - +
91D PHE* 3.9 12.1 - - - -
138D TYR* 2.7 40.7 + - + +
139D PHE 4.9 0.7 - - - +
140D ILE* 5.5 0.2 - - - -
141D PRO* 3.5 28.9 - - - +
147D LEU* 4.2 22.7 - - + +
148D ARG* 3.1 14.8 + - - +
150D LEU* 1.3 80.0 - - - +
152D ILE* 1.3 57.7 + - - +
155D MET* 2.9 38.9 + - - +
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Residues in contact with ILE 152 (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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147D LEU* 3.6 40.4 - - + +
148D ARG 3.1 13.3 + - - +
149D PRO* 3.8 13.0 - - + +
151D ASP* 1.3 76.7 - - - +
153D GLU* 1.3 59.0 + - + +
156D LYS* 3.0 29.9 + - + +
189D ASP* 5.6 2.2 - - + -
193D ASN* 3.3 48.0 - - + +
195D ILE* 3.8 11.7 - - + +
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Residues in contact with GLU 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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149D PRO 3.1 16.4 + - - +
150D LEU* 4.0 3.4 - - + +
152D ILE* 1.3 81.0 - - + +
154D PHE* 1.3 62.3 + - - +
156D LYS* 3.5 6.3 + - - +
157D ARG* 3.2 41.1 + - - +
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Residues in contact with PHE 154 (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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29D VAL* 4.1 7.0 - - + -
91D PHE* 3.6 45.5 - + + -
97D ASN 5.3 1.1 - - - -
100D CYS 4.4 0.2 - - - -
101D TRP* 3.5 44.4 - - + -
104D ILE* 4.1 15.9 - - + -
105D MET* 5.8 2.5 - - + -
138D TYR* 3.3 21.3 - + - +
150D LEU* 3.0 22.9 + - + +
151D ASP 3.8 0.2 - - - +
153D GLU* 1.3 78.4 - - - +
155D MET* 1.3 58.0 + - - +
157D ARG* 3.3 8.1 + - + +
158D LEU* 3.1 54.3 + - + +
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Residues in contact with MET 155 (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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138D TYR* 3.7 37.9 - - + -
140D ILE* 4.6 11.9 - - - -
147D LEU* 4.7 6.3 - - - -
151D ASP* 2.9 22.1 + - - +
154D PHE* 1.3 74.2 - - - +
156D LYS* 1.3 60.6 + - - +
158D LEU* 4.0 6.0 - - - +
159D SER* 2.9 33.8 + - - -
164D ILE* 3.7 19.5 - - + +
166D PRO* 3.6 31.2 - - + -
190D LEU* 3.6 25.1 - - + -
195D ILE* 3.9 19.4 - - + +
197D VAL* 4.2 0.4 - - + -
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Residues in contact with LYS 156 (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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152D ILE* 3.0 21.3 + - + +
153D GLU* 3.7 8.5 - - - +
155D MET* 1.3 77.1 - - - +
157D ARG* 1.3 62.7 + - + +
159D SER* 3.3 16.0 + - - -
160D LYS* 3.7 10.6 + - - +
193D ASN* 5.5 3.8 - - + +
195D ILE* 4.4 15.0 - - + +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D GLU* 5.4 12.5 + - - +
101D TRP* 4.0 27.1 + - - +
105D MET* 4.3 24.4 - - + +
153D GLU* 3.2 24.6 + - - +
154D PHE* 3.7 9.2 - - + +
156D LYS* 1.3 77.5 - - + +
158D LEU* 1.3 63.7 + - + +
160D LYS* 3.3 17.3 + - - +
161D VAL* 3.6 12.4 - - - +
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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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29D VAL* 4.0 9.6 - - + -
104D ILE* 4.4 16.8 - - + -
105D MET* 3.8 22.0 - - - -
108D ILE* 4.8 7.4 - - + -
136D CYS* 4.2 8.1 - - - -
138D TYR* 3.9 21.1 - - + -
154D PHE* 3.1 43.3 + - + +
155D MET* 3.4 2.2 + - - +
157D ARG* 1.3 74.4 - - - +
159D SER* 1.3 61.9 + - - +
161D VAL* 3.0 7.4 + - + +
162D VAL* 2.8 43.4 + - + +
164D ILE* 3.7 21.5 - - + -
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Residues in contact with SER 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 MET 2.9 19.4 + - - -
156D LYS* 3.3 11.6 + - - -
158D LEU* 1.3 75.2 - - - +
160D LYS* 1.3 62.5 + - - +
161D VAL 3.2 0.4 + - - -
162D VAL 3.4 17.3 - - - +
164D ILE* 3.8 8.2 - - - +
194D GLY 5.3 0.5 + - - -
195D ILE* 4.3 6.8 - - - +
196D ASP* 3.3 41.1 + - - +
200D GLN* 5.5 1.2 + - - -
281D HIS* 3.6 11.3 - - - -
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Residues in contact with LYS 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 LYS 3.8 10.1 - - - +
157D ARG* 3.3 12.7 + - - +
158D LEU 3.1 1.0 - - - -
159D SER* 1.3 79.8 + - - +
161D VAL* 1.3 64.5 - - + +
281D HIS* 4.2 7.5 + - - -
284D ALA* 5.6 5.4 - - - +
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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