Contacts of the strand formed by residues 208 - 216 (chain A) in PDB entry 5MJ3
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.7 22.4 - - + -
158A SER* 3.4 21.3 - - - +
159A SER 3.4 4.5 - - - +
160A ARG* 3.6 47.3 - - + +
168A VAL* 4.3 11.9 - - + -
195A GLU* 4.5 5.6 - - + +
206A LEU 3.9 0.2 + - - -
207A PRO* 1.3 72.7 - - - +
209A GLU* 1.3 65.3 + - - +
210A VAL* 4.1 0.2 - - + -
225A SER 3.8 0.5 - - - +
226A SER* 3.2 6.1 + - - -
227A PHE* 2.7 56.2 + - + +
229A ILE* 4.1 19.3 - - + -
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Residues in contact with GLU 209 (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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158A SER* 2.8 24.4 + - - -
159A SER* 2.8 29.2 + - - +
161A GLY 4.2 20.9 - - - +
162A SER* 4.5 16.2 + - - +
207A PRO* 3.6 16.5 - - - +
208A ILE* 1.3 72.6 - - - +
210A VAL* 1.3 58.5 + - - +
211A MET* 3.8 13.2 - - + +
224A THR* 5.4 5.7 - - - -
225A SER 3.5 3.8 - - - +
226A SER* 2.8 33.9 + - - -
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Residues in contact with VAL 210 (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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129A LEU* 4.4 6.4 - - + +
140A PHE* 3.6 30.1 - - + -
142A CYS* 4.0 18.2 - - + -
156A VAL* 4.2 17.7 - - + -
157A LYS 3.6 8.1 - - - +
158A SER* 4.0 5.6 - - - +
193A CYS* 5.5 1.1 - - - -
208A ILE* 4.1 0.2 - - + -
209A GLU* 1.3 77.9 - - - +
211A MET* 1.3 64.1 + - - +
212A VAL* 4.3 12.8 - - + -
224A THR* 3.1 9.4 - - - -
225A SER* 2.8 40.4 + - - +
227A PHE* 3.8 20.4 - - + -
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Residues in contact with MET 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER 3.7 0.7 - - - +
156A VAL* 3.4 4.9 - - - +
157A LYS* 2.8 62.7 + - + +
158A SER* 3.9 12.6 - - - +
159A SER* 4.2 7.6 - - - +
209A GLU* 3.8 27.4 - - + +
210A VAL* 1.3 76.9 - - - +
212A VAL* 1.3 63.0 + - - +
213A ASP* 4.2 0.6 + - - -
222A ASN* 6.6 0.2 - - + -
223A TYR 3.5 4.3 - - - +
224A THR* 4.1 16.4 - - + -
1D NAG 4.1 29.4 - - + -
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Residues in contact with VAL 212 (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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117A LEU* 5.1 1.3 - - + -
129A LEU* 3.8 28.5 - - + -
144A TRP* 3.9 35.0 - - + -
154A PHE* 4.2 18.2 - - + -
155A SER 3.4 5.2 - - - +
156A VAL* 4.2 7.4 - - + -
210A VAL* 4.3 8.7 - - + -
211A MET* 1.3 77.9 - - - +
213A ASP* 1.3 75.1 + - - +
222A ASN* 3.1 7.3 - - - +
223A TYR* 2.9 48.8 + - + +
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Residues in contact with ASP 213 (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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26A LEU* 3.6 16.9 - - + +
153A THR 4.5 0.2 - - - -
154A PHE* 3.2 6.9 - - - -
155A SER* 2.9 48.6 + - - +
157A LYS* 5.9 2.9 - - - +
211A MET 4.2 0.8 - - - -
212A VAL* 1.3 78.2 - - - +
214A ALA* 1.3 60.5 + - - +
215A VAL* 4.3 2.9 - - + -
220A TYR* 2.6 39.9 + - + -
221A GLU 3.7 2.9 - - - -
222A ASN* 3.7 5.9 - - - +
407A PG4 4.6 8.6 - - - +
1D NAG 4.0 11.3 - - - +
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Residues in contact with ALA 214 (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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116A ILE* 3.8 23.3 - - + +
153A THR 3.5 4.7 - - - -
154A PHE* 3.7 23.1 - - + -
212A VAL* 4.0 0.4 + - + -
213A ASP* 1.3 74.7 - - - +
215A VAL* 1.3 65.6 + - - +
219A LYS 3.7 0.9 - - - +
220A TYR* 3.5 0.7 - - - -
221A GLU 2.9 36.6 + - - +
223A TYR* 4.1 18.2 - - + -
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Residues in contact with VAL 215 (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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103A LEU* 3.9 35.2 - - + -
116A ILE* 4.3 0.4 - - - -
151A ASP 3.5 2.1 - - - +
152A LEU* 3.5 5.4 - - - +
153A THR* 2.9 38.1 + - - +
213A ASP* 5.3 1.3 - - + -
214A ALA* 1.3 80.4 - - - +
216A HIS* 1.3 59.9 + - - +
217A LYS 3.4 23.6 - - - +
219A LYS 3.2 9.4 - - - +
220A TYR* 4.0 13.7 - - + -
407A PG4 4.0 32.1 - - - +
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Residues in contact with HIS 216 (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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116A ILE* 3.7 23.1 - - + +
148A ILE* 3.4 42.4 - - + +
150A THR 3.5 14.2 + - - -
151A ASP 3.4 15.0 - - - -
152A LEU* 4.3 3.8 - - + -
215A VAL* 1.3 73.1 - - - +
217A LYS* 1.3 91.7 + - + +
219A LYS* 2.9 41.3 + - + +
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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