Contacts of the helix formed by residues 148 - 160 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A SER* 5.7 3.8 - - - +
93A ASP* 3.6 27.1 - - + +
31B GLN* 5.5 4.9 - - - +
141B PRO* 6.5 0.7 - - + -
146B SER 3.5 3.1 + - - +
147B LEU* 1.3 75.1 - - - +
149B PRO* 1.3 75.3 - - + +
150B LEU* 3.0 4.6 + - + +
151B ASP* 3.1 15.9 + - - +
152B ILE* 3.1 22.0 + - - +
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Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.7 17.5 - - + +
94A HIS* 3.7 35.7 - - + +
95A ILE 5.9 0.2 - - - -
147B LEU 3.9 3.6 - - - +
148B ARG* 1.3 86.5 - - + +
150B LEU* 1.3 61.0 + - - +
152B ILE* 3.8 13.1 - - + +
153B GLU* 3.1 32.2 + - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY 4.5 7.4 - - - +
93A ASP* 2.8 21.5 + - - +
94A HIS 4.3 13.0 - - - +
95A ILE* 4.9 5.4 - - + +
31B GLN* 3.8 20.2 - - + +
91B PHE* 4.1 18.6 - - + -
92B GLY* 3.6 29.2 - - - -
97B ASN* 4.0 25.4 - - + +
148B ARG* 3.0 2.9 + - + -
149B PRO* 1.3 78.9 - - - +
151B ASP* 1.3 62.7 + - - +
153B GLU* 3.4 3.0 + - + +
154B PHE* 3.0 36.4 + - + +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLN* 4.0 15.1 + - - +
91B PHE* 3.9 12.8 - - - -
138B TYR* 2.7 39.0 + - + +
139B PHE 4.9 0.7 - - - +
140B ILE* 5.5 0.4 - - - -
141B PRO* 3.3 30.8 - - - +
147B LEU* 4.4 21.0 - - + +
148B ARG* 3.1 14.4 + - - +
150B LEU* 1.3 78.4 - - - +
152B ILE* 1.3 59.7 + - - +
155B MET* 2.9 37.9 + - - +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.5 40.6 - - + +
148B ARG 3.1 15.1 + - - +
149B PRO* 3.8 11.0 - - + +
151B ASP* 1.3 77.8 - - - +
153B GLU* 1.3 67.7 + - + +
156B LYS* 2.9 30.9 + - + +
189B ASP* 5.7 1.6 - - + -
193B ASN* 3.3 47.3 - - + +
195B ILE* 3.8 11.6 - - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 3.1 20.3 + - + +
150B LEU* 3.9 3.4 - - - +
152B ILE* 1.3 85.9 - - + +
154B PHE* 1.3 64.8 + - - +
156B LYS* 3.3 12.0 + - - +
157B ARG* 3.1 41.5 + - - +
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 5.2 0.7 - - + -
91B PHE* 3.6 49.1 - + + -
97B ASN 5.3 1.1 - - - -
101B TRP* 3.5 45.8 - - + -
104B ILE* 3.9 18.6 - - + -
105B MET* 5.6 2.9 - - - -
138B TYR* 3.2 22.7 - + - +
150B LEU* 3.0 23.1 + - + +
151B ASP 3.8 0.2 - - - +
152B ILE 3.3 0.2 - - - -
153B GLU* 1.3 77.2 - - - +
155B MET* 1.3 57.4 + - - +
157B ARG* 3.2 11.4 + - + +
158B LEU* 3.0 54.8 + - + +
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Residues in contact with MET 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B TYR* 3.6 38.4 - - + -
140B ILE* 4.6 11.4 - - - -
147B LEU* 4.9 4.3 - - - -
151B ASP* 2.9 22.7 + - - +
152B ILE 4.0 2.2 - - - +
154B PHE* 1.3 74.6 - - - +
156B LYS* 1.3 60.1 + - - +
158B LEU* 4.0 6.7 - - - +
159B SER* 2.9 34.0 + - - -
164B ILE* 3.8 18.3 - - + +
166B PRO* 3.6 31.9 - - + -
190B LEU* 3.6 25.8 - - + -
195B ILE* 3.9 17.3 - - + -
197B VAL* 4.1 0.4 - - + -
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ILE* 2.9 20.6 + - + +
153B GLU* 3.5 17.7 - - - +
154B PHE 3.2 0.2 - - - -
155B MET* 1.3 77.4 - - - +
157B ARG* 1.3 62.3 + - + +
159B SER* 3.4 15.7 + - - -
160B LYS* 3.8 9.4 + - - +
193B ASN 5.6 3.4 - - - +
195B ILE* 4.5 12.1 - - + +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 5.0 16.2 + - - +
101B TRP* 3.2 37.3 + - - +
102B GLN* 5.7 0.2 - - - +
105B MET* 4.4 24.9 - - + +
153B GLU* 3.1 29.4 + - - +
154B PHE* 3.5 10.5 - - + +
156B LYS* 1.3 77.1 - - + +
158B LEU* 1.3 62.3 + - + +
160B LYS* 3.3 18.2 + - - +
161B VAL* 3.6 12.6 - - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.9 12.3 - - + -
104B ILE* 4.6 5.4 - - + -
105B MET* 4.0 15.5 - - - -
108B ILE* 3.7 29.8 - - + -
136B CYS* 4.4 2.7 - - - -
138B TYR* 3.7 18.2 - - + -
154B PHE* 3.0 44.4 + - + +
155B MET* 3.4 2.7 + - - +
157B ARG* 1.3 72.8 - - - +
159B SER* 1.3 60.3 + - - +
160B LYS 3.1 2.2 - - - -
161B VAL* 3.0 4.1 + - + +
162B VAL* 2.8 40.2 + - + +
164B ILE* 3.6 27.8 - - + -
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B MET 2.9 19.0 + - - -
156B LYS* 3.4 11.6 + - - -
158B LEU* 1.3 75.2 - - - +
160B LYS* 1.3 63.2 + - - +
161B VAL 3.2 0.9 + - - -
162B VAL 3.6 13.7 - - - +
164B ILE* 4.0 7.4 - - - +
194B GLY 5.1 1.2 + - - -
195B ILE* 4.3 7.0 - - - +
196B ASP* 3.3 42.7 + - - +
200B GLN* 5.4 1.0 + - - -
281B HIS* 3.8 11.4 - - - -
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LYS 3.9 9.9 - - - +
157B ARG* 3.3 12.7 + - - +
158B LEU 3.1 1.0 - - - -
159B SER* 1.3 81.5 + - - +
161B VAL* 1.3 64.2 - - + +
281B HIS* 4.4 6.5 + - - -
284B ALA* 5.2 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
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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