Contacts of the helix formed by residues 148 - 160 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C GLN* 2.7 47.0 + - - +
141C PRO* 3.3 20.7 - - - +
143C THR* 4.5 12.1 - - + +
146C SER 4.5 5.8 - - - +
147C LEU* 1.3 77.8 - - - +
149C PRO* 1.3 75.5 - - + +
150C LEU* 3.0 4.4 + - - +
151C ASP* 2.9 44.9 + - - +
152C ILE* 3.2 11.1 + - - +
31D GLN* 3.9 9.3 + - - -
32D SER* 4.3 22.0 + - - +
91D PHE 5.6 0.2 + - - -
92D GLY 3.7 13.0 + - - -
93D ASP* 3.6 28.7 - - + +
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Residues in contact with PRO 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LEU 3.9 3.6 - - - +
148C ARG* 1.3 88.2 - - + +
150C LEU* 1.3 60.9 + - - +
152C ILE* 3.6 13.7 + - + +
153C GLU* 3.3 28.8 + - + +
93D ASP* 3.6 15.0 - - + +
94D HIS* 3.6 38.6 - - + +
95D ILE 5.5 0.9 - - - +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLN* 3.4 26.5 - - + +
91C PHE* 4.2 17.0 - - + -
92C GLY* 3.6 20.9 - - - -
97C ASN* 3.9 25.4 - - + +
148C ARG* 3.0 2.7 + - + +
149C PRO* 1.3 75.3 - - - +
151C ASP* 1.3 64.4 + - - +
153C GLU* 3.3 5.8 + - + +
154C PHE* 3.0 35.9 + - + +
92D GLY 4.5 4.5 - - - +
93D ASP* 2.8 22.4 + - - +
94D HIS 4.0 15.3 - - - +
95D ILE* 4.5 11.7 - - + +
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Residues in contact with ASP 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLN* 4.6 1.7 - - - +
91C PHE* 4.0 10.7 - - - -
138C TYR* 2.8 36.6 + - + +
139C PHE 5.0 0.7 - - - +
140C ILE* 4.9 0.6 - - - +
141C PRO* 3.6 14.1 - - - +
147C LEU* 4.6 21.4 - - + +
148C ARG* 2.9 45.4 + - - +
150C LEU* 1.3 77.8 - - - +
152C ILE* 1.3 60.2 + - - +
155C MET* 2.8 39.4 + - - +
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Residues in contact with ILE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LEU* 3.8 36.8 - - + +
148C ARG 3.2 14.0 + - - +
149C PRO* 3.8 12.3 - - + +
150C LEU 3.2 0.2 - - - -
151C ASP* 1.3 77.3 - - - +
153C GLU* 1.3 60.4 + - - +
155C MET 3.5 0.3 + - - -
156C LYS* 2.9 45.2 + - - +
189C ASP* 5.7 1.6 - - + -
193C ASN* 3.3 48.0 - - + +
195C ILE* 3.9 9.5 - - + +
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PRO* 3.3 17.5 + - + +
150C LEU* 3.3 4.9 + - + +
152C ILE* 1.3 80.5 - - + +
154C PHE* 1.3 66.2 + - - +
156C LYS* 2.8 35.4 + - - +
157C ARG* 3.1 41.7 + - - +
95D ILE* 6.0 8.7 - - + -
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Residues in contact with PHE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.1 8.1 - - + -
91C PHE* 3.6 44.9 - + + -
97C ASN* 5.2 1.6 - - + -
100C CYS 4.4 0.2 - - - -
101C TRP* 3.5 45.8 - - + -
104C ILE* 4.2 15.7 - - + -
105C MET* 5.8 2.7 - - - -
138C TYR* 3.2 21.8 - + - +
150C LEU* 3.0 21.6 + - + +
153C GLU* 1.3 78.4 - - - +
155C MET* 1.3 56.7 + - - +
157C ARG* 3.3 10.2 + - + +
158C LEU* 3.0 54.6 + - + +
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Residues in contact with MET 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C TYR* 3.6 41.3 - - + -
140C ILE* 4.6 11.7 - - - -
147C LEU* 4.8 4.9 - - - -
151C ASP* 2.8 22.9 + - - +
152C ILE 4.0 2.5 - - - +
154C PHE* 1.3 74.6 - - - +
156C LYS* 1.3 59.9 + - - +
158C LEU* 4.4 6.3 - - - -
159C SER* 3.0 32.2 + - - -
164C ILE* 3.6 21.0 - - + +
166C PRO* 3.5 33.0 - - + -
190C LEU* 3.6 25.6 - - + -
195C ILE* 3.9 12.1 - - + +
197C VAL* 4.3 0.2 - - + -
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 2.9 29.1 + - + +
153C GLU* 2.8 40.6 + - - +
154C PHE 3.2 0.2 - - - -
155C MET* 1.3 78.9 - - - +
157C ARG* 1.3 61.5 + - + +
159C SER* 3.3 15.8 + - - -
160C LYS* 3.8 9.7 + - - +
193C ASN* 3.7 22.7 + - - +
194C GLY 5.4 1.1 - - - +
195C ILE* 3.6 22.0 - - + -
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 4.7 11.1 + - - +
101C TRP* 3.1 40.0 + - - +
102C GLN* 4.9 1.4 - - - +
105C MET* 4.5 24.3 - - + +
153C GLU* 3.1 27.6 + - - +
154C PHE* 3.6 11.2 - - + +
156C LYS* 1.3 77.0 - - + +
158C LEU* 1.3 62.8 + - + +
160C LYS* 3.3 18.2 + - - +
161C VAL* 3.6 12.3 - - - +
95D ILE* 4.4 20.4 - - - +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.0 8.7 - - + -
104C ILE* 4.5 6.5 - - + -
105C MET* 4.1 13.2 - - - -
108C ILE* 3.8 30.1 - - + -
136C CYS* 4.2 13.7 - - - -
138C TYR* 3.7 24.0 - - + -
154C PHE* 3.0 46.3 + - + +
155C MET* 4.0 2.7 - - - +
156C LYS 3.4 0.2 - - - -
157C ARG* 1.3 76.4 - - + +
159C SER* 1.3 59.8 + - - +
161C VAL* 3.0 4.4 + - - +
162C VAL* 2.8 40.0 + - + +
164C ILE* 3.7 13.5 - - + -
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Residues in contact with SER 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C MET 3.0 16.0 + - - -
156C LYS* 3.3 15.1 + - - -
158C LEU* 1.3 76.8 - - - +
160C LYS* 1.3 62.7 + - - +
161C VAL 3.5 0.2 + - - -
162C VAL 3.5 8.6 - - - +
164C ILE* 3.6 12.9 - - - +
194C GLY 5.3 0.7 + - - -
195C ILE* 4.3 2.6 - - - +
196C ASP* 3.3 41.8 + - - +
200C GLN* 5.4 0.5 + - - -
281C HIS* 3.5 19.9 - - - -
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Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C LYS 3.9 9.0 - - - +
157C ARG* 3.3 12.9 + - - +
158C LEU 3.1 0.6 - - - -
159C SER* 1.3 81.0 + - - +
161C VAL* 1.3 64.8 + - + +
281C HIS* 4.2 7.8 + - - +
284C ALA* 5.2 9.4 - - - +
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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