Contacts of the strand formed by residues 157 - 166 (chain B) in PDB entry 1M93
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 GLU 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.5 1.2 - - - -
153B VAL* 3.0 38.8 + - + +
154B SER* 3.1 24.6 + - - +
155B PRO 3.6 0.2 - - - -
156B THR* 1.4 79.8 - - - +
158B MET* 1.3 63.4 - - - +
159B VAL* 4.0 21.0 - - + +
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Residues in contact with MET 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PRO* 3.9 25.1 - - + -
151B PHE 3.3 4.5 - - - -
152B TYR* 3.5 46.0 - - + -
156B THR 4.1 2.6 + - - +
157B GLU* 1.3 76.3 - - - +
159B VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 4.7 1.8 - - - -
151B PHE* 2.8 34.4 + - - +
153B VAL* 4.0 17.3 - - + -
157B GLU* 4.0 22.7 - - + +
158B MET* 1.3 80.3 - - - +
160B ASP* 1.3 69.9 + - - +
337C SER* 4.9 3.6 - - - +
338C PRO* 3.6 32.1 - - + +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 3.2 40.0 - - - +
149B TYR 3.7 7.5 + - - +
150B PRO* 5.0 0.7 - - - -
159B VAL* 1.3 78.5 - - - +
161B VAL* 1.3 66.5 + - - +
162B SER* 4.6 1.9 + - - -
338C PRO* 3.5 16.8 - - - +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 3.3 4.9 - - - -
149B TYR* 2.9 45.4 + - + +
151B PHE* 4.2 19.1 - - + -
159B VAL 3.4 0.2 + - - -
160B ASP* 1.3 79.3 - - - +
162B SER* 1.3 70.2 + - - +
163B MET* 3.9 27.8 - - + -
236B PRO* 3.6 21.3 - - + -
237B LYS 4.6 4.5 - - - +
335C TYR* 3.4 25.1 - - - +
338C PRO* 4.4 4.7 - - + -
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 4.3 15.6 - - - +
147B SER 3.8 6.5 - - - -
148B ASP* 4.2 9.8 + - - +
160B ASP* 4.6 2.0 + - - -
161B VAL* 1.3 76.7 - - - +
163B MET* 1.3 58.4 + - - +
236B PRO* 3.5 4.0 - - - +
237B LYS* 3.0 41.6 + - - +
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Residues in contact with MET 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE 4.0 1.7 - - - +
146B THR* 3.3 4.2 - - - -
147B SER* 2.8 30.1 + - - -
149B TYR* 3.5 52.2 - - + -
151B PHE* 5.2 0.2 - - + -
161B VAL* 3.4 17.9 + - + -
162B SER* 1.3 71.8 - - - +
164B MET* 1.3 71.7 - - - +
165B SER* 3.9 1.8 + - - +
234B HIS* 3.6 15.9 - - + +
235B ILE* 3.3 37.2 - - - -
236B PRO* 3.5 5.8 - - + -
314C ALA 3.6 19.3 - - - +
315C ASP* 3.9 15.0 - - + -
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TRP* 5.0 0.7 - - + +
141B PHE* 3.6 31.3 - - + -
146B THR* 3.9 18.4 - - + +
163B MET* 1.3 74.8 - - - +
165B SER* 1.3 61.0 + - - +
233B VAL 3.8 0.3 - - - +
234B HIS* 3.1 5.4 - - - -
235B ILE* 2.8 58.8 + - + +
236B PRO 3.8 12.3 - - - +
237B LYS* 3.9 17.0 - - + -
286B VAL* 3.9 18.2 - - + -
287B ASN* 3.4 33.4 - - - +
288B GLU* 3.5 13.9 - - + +
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 3.9 7.7 - - - +
142B GLU 4.8 6.1 + - - +
145B PHE* 3.6 37.5 + - - +
146B THR* 4.9 0.2 + - - -
149B TYR* 3.9 7.6 + - - -
163B MET* 3.9 6.0 + - - +
164B MET* 1.3 78.0 + - - +
166B MET* 1.3 63.3 + - - +
167B TYR* 3.4 25.7 + - - -
233B VAL 3.2 4.5 - - - -
234B HIS* 2.6 29.1 + - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 3.3 27.6 - - + +
140B PRO 3.2 31.6 - - - +
141B PHE* 3.8 27.8 - - + +
142B GLU* 5.2 7.0 - - - +
145B PHE* 5.2 2.0 - - - -
165B SER* 1.3 76.0 - - - +
167B TYR* 1.3 67.3 + - - +
169B GLU* 3.9 24.9 - - + +
171B PHE* 3.7 27.8 - - + -
231B ILE 4.4 1.2 - - - +
232B ASP* 3.4 4.0 - - - +
233B VAL* 2.8 38.3 + - + +
234B HIS* 5.0 0.2 + - - -
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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