Contacts of the strand formed by residues 187 - 195 (chain B) in PDB entry 1ML3
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A LEU* 4.1 8.1 - - + -
323A GLU* 4.0 21.1 - - - +
326A PHE* 3.5 30.7 - - + +
185B VAL* 3.6 6.4 - - - +
186B GLN* 1.3 86.8 - - + +
188B GLY* 1.3 59.7 + - - +
242B LYS* 3.5 9.2 - - + +
262B PHE* 3.1 21.7 - - - +
263B THR* 2.8 29.9 + - - +
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Residues in contact with GLY 188 (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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320A LEU* 4.5 1.3 - - - +
326A PHE* 3.7 2.6 - - - -
185B VAL* 4.4 1.3 - - - +
187B THR* 1.3 79.3 - - - +
189B LEU* 1.3 68.3 + - - +
242B LYS 2.9 10.5 + - - +
243B LEU* 3.2 16.2 - - - -
244B THR 3.2 22.6 + - - -
260B LEU* 4.8 4.9 - - - -
261B THR 3.4 9.2 - - - -
262B PHE* 4.0 5.4 - - - -
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Residues in contact with LEU 189 (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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261A THR* 4.3 9.0 - - + +
318A ASN 4.2 9.4 - - - +
319A ASN* 4.3 3.6 - - - +
320A LEU* 4.3 8.3 - - + +
326A PHE* 3.4 35.4 - - + +
327A PHE 3.9 15.0 - - - +
328A LYS* 3.8 37.5 - - + +
188B GLY* 1.3 77.1 - - - +
190B MET* 1.3 60.4 + - - +
244B THR* 3.2 38.6 - - + +
245B GLY* 4.7 1.3 - - - +
259B ASP 4.0 0.9 - - - +
260B LEU* 3.6 3.2 - - - +
261B THR* 2.9 34.1 + - - +
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Residues in contact with MET 190 (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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328A LYS* 4.5 1.6 - - - -
167B THR* 3.4 33.9 - - + -
171B LEU* 3.4 42.4 - - + -
189B LEU* 1.3 76.2 - - - +
191B THR* 1.3 72.2 + - - +
192B THR* 4.3 4.3 - - - -
226B THR* 5.0 2.9 - - + -
228B ALA* 4.0 10.8 - - + -
229B ALA* 3.8 13.0 - - + +
244B THR 2.9 8.2 + - - +
245B GLY* 2.9 16.2 - - - -
246B MET 2.9 36.2 + - - +
258B VAL* 4.1 9.2 - - + -
259B ASP 3.6 5.6 - - - +
260B LEU* 4.2 15.9 - - + -
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Residues in contact with THR 191 (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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193A ILE* 4.9 2.7 - - + -
259A ASP* 2.5 30.8 + - - +
328A LYS* 3.0 19.9 + - - -
190B MET* 1.3 74.5 + - - +
192B THR* 1.3 60.7 + - - +
193B ILE* 4.2 14.4 - - + -
246B MET* 3.7 8.3 - - + +
248B PHE* 3.5 26.7 - - + -
257B VAL 3.9 0.2 - - - +
258B VAL 3.6 0.2 - - - -
259B ASP* 2.6 54.4 + - + +
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Residues in contact with THR 192 (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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167B THR* 4.5 9.4 - - + +
190B MET* 4.4 13.9 - - - -
191B THR* 1.3 76.4 - - - +
193B ILE* 1.3 63.4 + - - +
194B HIS* 3.1 16.4 + - + -
226B THR* 5.0 3.4 - - + -
246B MET 3.2 17.0 + - - +
247B SER* 3.4 18.8 - - - +
248B PHE* 3.0 21.7 + - - +
257B VAL 3.3 11.1 + - - -
258B VAL* 4.5 3.1 - - - -
333B TYR* 3.2 23.1 + - - -
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Residues in contact with ILE 193 (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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193A ILE* 4.0 22.4 - - + -
221A ILE* 3.5 26.7 - - + +
248A PHE* 3.9 34.1 - - + -
250A VAL* 3.9 12.3 - - + -
191B THR* 4.2 10.3 - - + -
192B THR* 1.3 71.1 - - - +
194B HIS* 1.3 59.9 + - - +
248B PHE* 3.6 4.9 - - + -
250B VAL* 3.9 22.0 - - + -
256B SER* 3.4 4.3 - - - -
257B VAL* 2.9 48.0 + - + +
259B ASP* 4.2 15.0 - - + +
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Residues in contact with HIS 194 (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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167B THR* 4.2 5.6 - - - -
192B THR* 3.1 10.5 + - + +
193B ILE* 1.3 74.9 - - - +
195B SER* 1.3 82.8 + - - +
197B THR* 3.9 13.5 - - + -
247B SER* 3.7 12.6 - - - +
248B PHE 2.7 9.6 + - - +
249B ARG* 3.0 32.5 + - - -
250B VAL* 2.5 36.4 + - - -
256B SER* 3.5 13.4 + - - -
333B TYR* 3.3 24.1 + - - -
335B ASN* 4.2 7.0 - - - +
1166B CYX 2.6 40.1 + - + +
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Residues in contact with SER 195 (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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221A ILE* 5.1 0.2 - - - +
193B ILE 4.3 0.2 + - - -
194B HIS* 1.3 94.9 + - - +
196B TYR* 1.3 64.7 + - - +
197B THR* 3.8 0.5 - - - +
249B ARG* 4.0 1.0 - - - -
250B VAL 3.6 1.3 - - - -
252B THR* 2.9 42.8 + - - -
253B PRO 3.8 2.4 + - - -
254B ASP* 3.3 23.1 - - - -
255B VAL 3.4 12.8 + - - -
256B SER* 3.4 4.1 + - - -
335B ASN* 3.5 13.2 + - - -
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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