Contacts of the strand formed by residues 189 - 198 (chain F) in PDB entry 5MWF
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 HIS 189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F ALA 3.8 0.7 - - - +
37F LEU* 3.0 27.5 - - - +
38F ARG* 3.2 47.5 + - + +
182F HIS* 4.6 13.9 - + + +
183F PHE 3.3 4.9 - - - +
184F SER* 3.0 35.0 + - - -
185F GLY 4.1 6.3 + - - -
187F VAL 5.5 1.5 - - - -
188F ALA* 1.3 82.5 - - - +
190F LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 3.9 20.6 - - + -
36F ALA 3.5 3.8 - - - -
37F LEU* 3.5 25.8 - - + -
71F VAL* 5.1 6.1 - - + -
146F VAL* 4.1 26.9 - - + -
147F GLU 5.7 0.4 - - - -
148F ALA* 5.3 8.3 - - + -
164F GLU* 4.4 5.8 - - + -
166F VAL* 4.1 25.4 - - + -
182F HIS* 2.8 25.3 - - - -
183F PHE* 2.8 33.9 + - + +
188F ALA* 4.0 18.4 - - + +
189F HIS* 1.3 73.4 - - - +
191F GLU* 1.3 57.7 + - - +
192F LEU* 5.2 2.7 - - + -
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Residues in contact with GLU 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 3.3 9.1 - - - +
35F SER* 2.8 43.5 + - - +
36F ALA* 3.1 25.2 + - + +
180F SER* 5.1 6.8 + - - +
181F LEU 3.5 8.8 - - - +
182F HIS* 3.1 36.3 + - + +
183F PHE* 5.8 0.2 - - - -
190F LEU* 1.3 71.4 - - - +
192F LEU* 1.3 60.9 - - - +
193F GLN* 5.0 3.9 + - - +
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 3.8 16.8 - - + -
33F GLN 3.1 20.0 - - - +
34F LEU* 4.2 8.5 - - + -
144F LEU* 4.6 1.3 - - + -
146F VAL* 3.6 36.3 - - + -
180F SER* 3.8 0.7 + - - -
181F LEU* 2.9 62.3 + - + +
183F PHE* 4.3 14.8 - - + -
190F LEU* 5.2 2.9 - - + -
191F GLU* 1.3 77.0 - - - +
193F GLN* 1.3 69.1 + - - +
194F ILE* 3.8 18.8 - - + -
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Residues in contact with GLN 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU 3.7 0.9 - - - +
32F LEU* 3.6 4.5 - - - -
33F GLN* 3.2 46.7 + - - +
35F SER* 3.4 28.3 + - - -
106F PRO 5.4 2.5 + - - +
178F TRP* 3.7 34.8 - - + -
179F LYS 3.3 8.3 - - - +
180F SER* 4.2 21.1 + - - +
191F GLU* 4.8 3.4 + - - +
192F LEU* 1.3 80.7 + - - +
194F ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F PHE* 3.8 26.0 - - + -
31F GLU 3.3 5.2 - - - +
32F LEU* 4.3 4.0 - - + -
142F PHE* 3.7 33.9 - - + -
144F LEU* 4.0 10.1 - - + -
168F HIS* 4.9 3.4 - - + +
172F ILE* 3.8 17.5 - - + +
177F ARG 3.3 1.7 - - - +
178F TRP* 3.3 2.8 - - - -
179F LYS* 3.0 40.4 + - + +
181F LEU* 3.9 16.2 - - + -
192F LEU* 3.8 20.0 - - + -
193F GLN* 1.3 77.3 - - - +
195F ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F PHE* 3.5 5.2 - - - -
31F GLU* 2.9 51.8 + - + +
172F ILE* 4.0 4.4 - - - +
174F PRO 5.7 0.2 + - - -
177F ARG* 3.5 56.6 - - - +
178F TRP* 3.4 51.2 - - + +
194F ILE* 1.3 79.0 - - - +
196F VAL* 1.3 77.1 + - - +
197F ARG* 4.9 15.4 - - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR 3.3 11.7 - - - +
30F PHE* 3.7 22.7 - - + -
134F PHE* 4.0 20.2 - - + -
138F TRP* 4.0 18.8 - - + -
172F ILE* 3.9 23.6 - - + +
173F ASN 4.5 5.6 + - - +
174F PRO* 3.2 49.1 - - + +
177F ARG 4.7 0.6 + - - -
195F ARG* 1.3 86.3 + - - +
197F ARG* 1.3 65.1 + - - +
207F CYS* 4.7 1.6 - - - -
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Residues in contact with ARG 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLY* 3.1 2.6 - - - -
29F TYR* 3.0 85.0 + - + +
31F GLU* 3.0 48.4 + - - +
131F VAL* 3.6 13.1 - - - +
174F PRO* 5.0 1.8 - - - -
195F ARG* 4.3 18.3 - - - +
196F VAL* 1.3 75.7 - - - +
198F CYS* 1.3 65.3 + - - +
207F CYS* 4.0 6.7 - - - -
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Residues in contact with CYS 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F MET 3.6 1.3 - - - +
28F GLY* 4.2 0.2 - - - -
29F TYR* 4.6 1.9 - - - -
174F PRO* 4.4 9.8 - - - +
197F ARG* 1.3 84.2 - - - +
199F ASP* 1.3 65.5 + - - +
202F TYR 3.5 23.1 - - - +
203F TYR* 4.4 3.6 - - - -
204F SER 3.8 11.4 - - - -
207F CYS* 2.0 54.7 - - + -
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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