Contacts of the helix formed by residues 148 - 160 (chain A) in PDB entry 5CYO
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLN* 4.5 12.3 + - - +
141A PRO* 4.2 17.9 - - + +
143A THR* 3.4 26.7 - - + +
146A SER 4.6 5.8 - - - +
147A LEU* 1.3 77.7 - - - +
149A PRO* 1.3 73.8 - - + +
150A LEU* 4.3 7.2 - - + +
151A ASP* 3.1 21.0 + - - +
152A ILE* 2.9 20.8 + - - +
31B GLN* 3.9 32.9 + - - +
32B SER* 2.7 31.5 + - - -
34B LEU* 5.3 3.6 - - - +
92B GLY 5.2 0.4 - - - -
93B ASP* 4.1 31.6 + - - +
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU 3.8 3.8 - - - +
148A ARG* 1.3 83.9 - - - +
150A LEU* 1.3 55.0 + - - +
152A ILE* 3.3 12.9 + - + +
153A GLU* 2.8 31.4 + - - +
93B ASP* 3.5 24.2 - - + +
94B HIS* 4.3 17.9 - - + +
95B ILE* 4.1 16.6 - - + +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 4.4 9.4 - - - +
91A PHE* 3.8 21.1 - - + -
92A GLY* 3.6 31.6 - - - +
97A ASN* 4.3 9.6 - - + +
100A CYS* 3.7 22.2 - - - -
101A TRP* 4.2 13.9 - - + -
148A ARG* 3.2 5.5 + - + +
149A PRO* 1.3 78.5 - - - +
151A ASP* 1.3 60.9 + - - +
153A GLU* 3.3 1.7 + - - +
154A PHE* 2.8 29.0 + - + +
93B ASP 5.0 1.3 + - - +
94B HIS 5.2 2.9 - - - +
95B ILE* 3.7 35.2 - - + +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 4.7 11.7 + - - +
91A PHE* 3.9 10.4 - - - -
138A TYR* 2.4 41.3 + - + +
139A PHE 4.6 1.7 - - - +
140A ILE* 5.1 1.6 - - - +
141A PRO* 3.6 26.4 - - - +
147A LEU* 4.5 9.9 - - + -
148A ARG* 3.1 24.9 + - - +
150A LEU* 1.3 75.8 - - - +
152A ILE* 1.3 65.8 + - - +
155A MET* 2.9 39.1 + - + +
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.7 41.3 - - + +
148A ARG 2.9 15.2 + - - +
149A PRO* 3.5 11.0 - - + +
151A ASP* 1.3 77.7 - - - +
153A GLU* 1.3 57.9 + - - +
155A MET* 4.8 1.8 - - - -
156A LYS* 2.9 36.1 + - - +
189A ASP* 4.5 8.5 - - + +
193A ASN* 3.7 41.1 - - + +
195A ILE* 3.6 14.1 - - + +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 3.6 27.8 - - + -
149A PRO 2.8 17.4 + - - +
150A LEU 3.6 3.8 - - - +
152A ILE* 1.3 78.4 - - - +
154A PHE* 1.3 60.7 + - - +
156A LYS* 3.4 16.7 + - - +
157A ARG* 2.8 58.7 + - - +
95B ILE* 3.7 17.6 - - + +
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.2 3.8 - - + -
91A PHE* 3.3 46.4 - + - -
100A CYS* 4.2 7.6 - - - -
101A TRP* 3.5 48.4 - + + -
104A ILE* 3.8 27.4 - - + -
105A MET* 5.1 1.6 - - - -
138A TYR* 3.5 16.2 - + - +
150A LEU* 2.8 20.6 + - + +
153A GLU* 1.3 73.3 - - - +
155A MET* 1.3 58.4 + - - +
157A ARG* 3.3 6.0 + - + +
158A LEU* 2.9 56.8 + - + +
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Residues in contact with MET 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.5 46.7 - - + -
140A ILE* 4.3 3.6 - - + -
147A LEU* 3.6 42.6 - - + -
151A ASP 2.9 26.6 + - - +
152A ILE* 4.0 2.7 - - - +
154A PHE* 1.3 75.2 - - - +
156A LYS* 1.3 61.4 + - - +
158A LEU* 3.8 6.6 - - - +
159A SER* 2.9 32.7 + - - -
164A ILE* 4.5 11.8 - - + +
166A PRO* 4.2 15.0 - - - -
190A LEU* 3.9 15.0 - - + -
195A ILE* 3.9 14.2 - - + +
197A VAL* 5.8 0.2 - - - -
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 2.9 24.4 + - - +
153A GLU* 3.7 19.5 - - - +
154A PHE 3.2 0.2 - - - -
155A MET* 1.3 77.2 - - - +
157A ARG* 1.3 63.5 + - + +
159A SER* 2.7 23.1 + - - +
160A LYS* 3.5 34.0 - - - +
193A ASN* 3.5 46.1 + - - +
194A GLY 5.5 2.0 - - - +
195A ILE* 4.0 11.3 - - + +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN* 5.4 1.2 + - - -
101A TRP* 3.2 58.1 - - + +
105A MET* 3.7 28.3 - - + +
153A GLU* 2.8 40.4 + - - +
154A PHE* 3.7 4.7 - - + +
156A LYS* 1.3 82.6 - - + +
158A LEU* 1.3 62.5 + - - +
160A LYS* 3.4 24.2 + - - +
161A VAL* 3.9 1.7 - - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.1 3.1 - - + -
104A ILE* 4.2 6.1 - - + -
105A MET* 3.8 12.6 - - - -
108A ILE* 3.6 30.5 - - + -
136A CYS* 3.8 19.3 - - - -
138A TYR* 3.7 25.1 - - + -
154A PHE* 2.9 46.3 + - + +
155A MET* 3.8 3.8 - - - +
157A ARG* 1.3 76.8 - - - +
159A SER* 1.3 57.2 + - - +
160A LYS 3.0 0.2 - - - -
161A VAL* 2.9 9.4 + - - +
162A VAL* 2.9 36.6 + - + +
164A ILE* 3.5 13.5 - - + -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A MET 2.9 16.1 + - - -
156A LYS* 2.7 24.6 + - - +
158A LEU* 1.3 75.5 - - - +
160A LYS* 1.3 62.1 + - - +
161A VAL 3.6 0.3 + - - -
162A VAL 3.6 14.7 - - - +
164A ILE* 3.8 7.2 - - - +
194A GLY 5.0 1.9 + - - -
195A ILE* 4.0 14.6 - - - +
196A ASP* 3.8 27.8 + - - +
281A HIS* 3.9 11.4 - - - -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS* 3.5 39.0 + - - +
157A ARG* 3.4 14.3 + - + +
158A LEU 3.0 1.0 + - - -
159A SER* 1.3 81.2 + - - +
161A VAL* 1.3 64.3 + - + +
194A GLY 5.5 4.4 + - - -
281A HIS* 4.2 8.4 + - - +
284A ALA* 5.5 5.2 - - - +
288A LYS* 4.2 10.6 + - - +
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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