Contacts of the helix formed by residues 152 - 164 (chain E) in PDB entry 5IYB
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 THR 152 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E VAL 5.3 2.5 - - - +
151E MET* 1.3 74.4 - - - +
153E LYS* 1.3 57.1 + - - +
154E GLU* 4.2 5.8 + - - +
155E GLU* 2.6 61.6 + - - +
156E VAL* 3.3 7.4 + - - -
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Residues in contact with LYS 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E MET 3.8 2.0 + - - -
152E THR* 1.3 70.3 - - - +
154E GLU* 1.3 60.8 + - - +
156E VAL* 3.4 12.7 + - - +
157E THR* 3.1 31.2 + - - +
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Residues in contact with GLU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E THR* 2.8 10.7 + - - +
153E LYS* 1.3 74.4 - - - +
155E GLU* 1.3 65.5 + - + +
157E THR* 3.1 12.3 + - + -
158E GLU* 3.0 32.5 + - + +
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Residues in contact with GLU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A LEU* 5.8 0.3 - - - +
149E VAL* 6.0 1.4 - - - +
150E VAL 5.0 0.9 - - - +
151E MET* 3.4 29.7 - - + +
152E THR* 2.6 44.2 + - - +
154E GLU* 1.3 75.1 - - + +
156E VAL* 1.3 55.3 + - - +
158E GLU* 3.4 10.4 + - - +
159E LEU* 2.9 26.3 + - - +
192E LYS* 5.8 1.7 + - - -
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Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E MET* 3.8 30.1 - - + +
152E THR 3.3 6.7 + - - +
153E LYS* 3.5 14.4 - - - +
154E GLU 3.2 0.4 - - - -
155E GLU* 1.3 73.6 - - - +
157E THR* 1.3 66.7 + - - +
159E LEU* 3.0 8.8 + - + +
160E LEU* 2.9 43.6 + - + +
167E GLU* 5.2 8.1 - - + +
190E VAL* 4.0 35.4 - - + +
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Residues in contact with THR 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E LYS* 3.1 19.8 + - - +
154E GLU* 3.1 16.0 + - + -
156E VAL* 1.3 77.5 - - - +
158E GLU* 1.3 68.6 + - - +
160E LEU* 3.6 5.7 + - - +
161E ALA* 3.2 24.2 + - + +
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Residues in contact with GLU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A LEU* 5.9 0.9 - - + -
154E GLU* 3.0 27.5 + - + +
155E GLU* 3.5 11.9 - - - +
156E VAL 3.2 0.2 - - - -
157E THR* 1.3 83.2 - - - +
159E LEU* 1.3 56.3 + - - +
161E ALA* 3.4 6.4 + - - +
162E ARG* 3.0 75.8 + - - +
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Residues in contact with LEU 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A LEU* 3.7 24.6 - - + +
151E MET* 4.7 9.2 - - + -
155E GLU 2.9 14.9 + - - +
156E VAL* 3.0 10.9 + - + +
158E GLU* 1.3 74.3 - - - +
160E LEU* 1.3 77.7 + - + +
162E ARG* 4.2 0.2 - - - -
163E TYR* 3.3 36.7 + - + +
165E LEU* 5.4 2.2 - - + +
170E LEU* 5.0 10.5 - - + -
190E VAL* 5.1 4.0 - - + -
206E TYR* 3.6 62.6 - - + -
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Residues in contact with LEU 160 (chain E).
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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156E VAL* 2.9 35.1 + - + +
157E THR* 4.1 4.7 - - - +
159E LEU* 1.3 89.5 - - + +
161E ALA* 1.3 53.4 + - - +
164E LYS* 2.7 28.9 + - - -
165E LEU* 2.9 25.9 + - + +
166E ARG* 3.8 10.3 - - - +
167E GLU* 3.4 46.4 - - + +
170E LEU* 4.5 18.2 - - + -
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Residues in contact with ALA 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E THR* 3.2 20.4 + - + +
158E GLU* 3.7 11.0 - - - +
160E LEU* 1.3 78.4 - - - +
162E ARG* 1.3 65.9 + - + +
164E LYS* 3.1 21.8 + - - +
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Residues in contact with ARG 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A ASP* 2.3 49.6 + - - +
1028A PRO* 3.7 13.5 - - - +
1029A LEU* 2.9 49.8 - - + +
1030A SER* 4.8 10.2 + - - +
158E GLU* 3.0 56.7 + - - +
159E LEU 3.6 2.7 + - - +
161E ALA* 1.3 77.0 - - + +
163E TYR* 1.3 62.2 + - + +
164E LYS* 4.7 3.5 - - - +
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Residues in contact with TYR 163 (chain E).
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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876A ASP* 4.8 7.0 - - - +
878A THR* 4.5 19.5 - - + -
880A ARG* 4.7 3.1 + - - -
889A LEU* 3.2 40.7 - - + +
890A ARG* 5.1 8.6 + - - -
1023A VAL* 6.6 0.4 - - + -
1029A LEU* 4.5 12.9 - - + +
1030A SER* 6.0 3.5 - - - -
1033A ALA* 4.2 20.1 - - - +
159E LEU* 3.3 40.4 + - + +
161E ALA 3.3 0.2 - - - -
162E ARG* 1.3 80.0 - - + +
164E LYS* 1.3 69.2 + - - +
165E LEU* 3.5 33.7 - - + +
206E TYR* 4.9 2.8 + + - -
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Residues in contact with LYS 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880A ARG* 5.5 0.3 + - - -
160E LEU 2.7 16.7 + - - -
161E ALA* 3.1 16.0 + - - +
162E ARG 4.7 3.8 - - - +
163E TYR* 1.3 78.3 - - - +
165E LEU* 1.3 62.9 + - - +
169E GLN* 5.4 1.4 + - - +
110F LEU* 5.1 10.6 - - + +
112F ASP* 3.5 43.1 + - + +
114F SER* 3.7 14.5 + - - -
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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