Contacts of the strand formed by residues 153 - 161 (chain E) in PDB entry 4OA5
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 ILE 153 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E VAL* 5.2 0.4 - - + -
129E PRO* 4.5 0.4 - - - -
130E PHE* 3.4 26.0 - - + +
131E ASP 4.0 4.5 - - - +
132E MET 3.7 25.6 - - - +
133E ILE* 3.8 13.2 - - + +
148E TRP* 4.3 9.6 - - + -
149E ALA* 3.0 35.4 + - + +
150E LYS 4.5 0.3 - - - +
151E MET 4.6 2.0 - - - +
152E TYR* 1.3 81.4 + - - +
154E ARG* 1.3 70.4 + - - +
157E GLY* 3.8 21.3 - - - -
158E LEU 4.1 6.1 - - - +
159E ILE* 5.0 1.6 - - + -
216E LYS* 2.8 35.1 + - + -
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Residues in contact with ARG 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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94D VAL* 6.4 0.8 - - - +
98D ASN* 5.7 2.8 + - - -
111D THR* 5.1 3.1 - - - -
112D VAL 4.1 20.2 + - - -
113D LEU* 4.0 17.9 - - + +
114D HIS* 5.5 7.0 - - - +
55E ALA* 4.4 15.0 + - - +
56E GLY 5.1 3.6 + - - -
57E ILE* 4.6 5.9 - - - +
129E PRO* 4.0 20.2 - - + +
130E PHE 3.0 19.7 + - - +
131E ASP* 2.8 34.3 + - - +
153E ILE* 1.3 79.1 - - - +
155E LYS* 1.3 80.7 + - - +
156E GLY* 3.3 23.0 + - - -
157E GLY* 2.9 27.8 + - - +
216E LYS* 3.7 5.5 - - - +
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Residues in contact with LYS 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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113D LEU* 6.0 0.2 - - - -
114D HIS* 3.2 50.3 + - - +
115D GLY* 4.3 3.8 - - - -
120D GLN* 3.2 37.3 + - - +
123D THR* 5.8 3.3 - - + +
305D IOD 4.0 17.5 - - + -
153E ILE 3.8 0.6 + - - -
154E ARG* 1.3 95.0 + - - +
156E GLY* 1.3 59.7 + - - +
216E LYS* 4.0 3.0 - - - +
217E LEU 3.3 27.4 - - - +
218E THR* 3.4 29.1 + - - +
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Residues in contact with GLY 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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114D HIS* 6.1 3.4 - - - -
55E ALA* 5.8 2.8 - - - +
154E ARG* 3.3 16.5 + - - -
155E LYS* 1.3 74.8 - - - +
157E GLY* 1.3 63.8 + - - +
158E LEU* 4.8 4.7 - - - +
215E ILE* 3.9 15.9 - - - +
216E LYS 2.7 20.4 + - - -
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Residues in contact with GLY 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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57E ILE* 5.5 0.4 - - - -
131E ASP 3.1 15.3 - - - -
153E ILE* 3.8 8.1 - - - -
154E ARG* 2.9 26.7 + - - -
155E LYS 3.1 1.8 + - - -
156E GLY* 1.3 80.1 - - - +
158E LEU* 1.3 61.6 + - - -
215E ILE* 3.5 2.6 - - - -
216E LYS* 2.9 28.3 + - - +
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Residues in contact with LEU 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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51E LEU* 4.2 21.8 - - + +
55E ALA* 3.9 25.8 - - + -
57E ILE* 4.1 20.0 - - + -
131E ASP 2.9 7.3 + - - -
132E MET* 3.2 22.8 - - + -
133E ILE* 3.0 26.2 + - - +
153E ILE* 4.1 2.3 - - - +
156E GLY 4.8 3.1 - - - +
157E GLY* 1.3 74.8 - - - -
159E ILE* 1.3 63.9 + - - +
160E VAL* 4.0 11.0 - - + -
213E VAL* 5.0 9.4 - - + -
214E SER 3.3 13.0 - - - +
215E ILE* 3.8 22.9 - - + -
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Residues in contact with ILE 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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133E ILE* 3.7 21.3 - - + -
135E ILE* 4.4 15.0 - - + -
146E LEU* 3.9 25.6 - - + -
149E ALA* 4.2 12.8 - - + -
150E LYS* 5.5 0.7 - - + +
153E ILE* 5.0 4.0 - - + -
158E LEU* 1.3 77.9 - - - +
160E VAL* 1.3 62.5 + - - +
190E PHE* 4.6 4.3 - - + -
194E LEU* 4.2 21.3 - - + -
200E TYR* 4.1 21.3 - - + -
212E MET* 3.8 3.1 - - + +
213E VAL* 3.7 1.6 - - - -
214E SER* 2.8 45.3 + - - +
216E LYS* 4.3 20.9 - - + -
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Residues in contact with VAL 160 (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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48E LEU* 3.9 18.8 - - + -
51E LEU* 4.4 13.5 - - + -
132E MET* 3.9 21.1 - - + -
133E ILE 2.9 10.8 + - - +
134E PHE* 3.2 20.4 - - + -
135E ILE* 2.7 33.1 + - - +
158E LEU* 4.3 14.6 - - + -
159E ILE* 1.3 78.6 - - - +
161E ALA* 1.3 58.9 + - - +
211E MET* 3.9 12.3 - - + -
212E MET 3.2 13.0 - - - +
213E VAL* 4.4 10.3 - - + -
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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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134E PHE* 4.5 0.9 - - - -
135E ILE* 3.2 17.3 - - + +
142E TYR* 3.8 13.5 - - + -
160E VAL* 1.3 77.9 - - - +
162E ASP* 1.3 62.5 + - - +
164E THR* 3.6 6.8 - - + +
190E PHE* 3.7 29.8 - - + -
211E MET* 3.5 5.8 - - - -
212E MET* 2.8 38.7 + - + +
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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