Contacts of the strand formed by residues 189 - 198 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.1 8.1 - - - +
38B ARG* 3.0 59.4 + - + -
183B PHE 3.3 5.8 + - - +
184B SER* 3.2 29.4 - - - -
185B GLY 5.6 2.7 + - - -
187B VAL 5.2 2.7 - - - -
188B ALA* 1.3 78.8 - - - +
190B LEU* 1.3 65.2 + - - +
191B GLU* 5.8 2.0 - - + +
408B CL 4.3 12.3 - - - +
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Residues in contact with LEU 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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34B LEU* 4.1 16.2 - - + -
36B ALA 3.4 4.9 - - - +
37B LEU* 3.9 24.9 - - + -
71B VAL* 5.2 3.6 - - + -
146B VAL* 4.0 28.3 - - + +
147B GLU 5.8 0.9 - - - -
148B ALA* 5.3 4.0 - - + -
164B GLU* 4.5 14.4 - - + -
166B VAL* 4.4 15.0 - - + -
182B HIS* 3.8 0.3 - - - -
183B PHE* 2.7 51.4 + - + +
188B ALA* 4.0 19.7 - - + +
189B HIS* 1.3 81.0 - - - +
191B GLU* 1.3 71.5 + - - +
192B LEU* 4.3 3.4 - - + -
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Residues in contact with GLU 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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34B LEU* 3.6 4.2 - - - +
35B SER* 3.0 33.5 + - - +
36B ALA* 3.0 33.3 + - + -
180B SER* 4.6 2.9 + - - -
181B LEU 3.7 3.4 - - - +
182B HIS* 2.6 46.0 + - - +
183B PHE 5.4 0.2 - - - +
189B HIS* 5.8 2.1 - - + +
190B LEU* 1.3 80.2 - - - +
192B LEU* 1.3 62.2 + - - +
193B GLN* 4.5 2.5 + - - +
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Residues in contact with LEU 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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32B LEU* 4.3 12.3 - - + -
33B GLN 3.1 17.7 - - - +
34B LEU* 4.1 18.6 - - + -
144B LEU* 4.6 2.2 - - + -
146B VAL* 4.2 26.7 - - + -
180B SER* 3.6 1.7 + - - -
181B LEU* 2.8 49.2 + - + +
183B PHE* 3.7 35.0 - - + -
190B LEU* 4.5 4.5 - - + -
191B GLU* 1.3 75.5 - - - +
193B GLN* 1.3 68.4 + - - +
194B ILE* 3.9 16.8 - - + -
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Residues in contact with GLN 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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32B LEU* 3.4 2.6 - - - -
33B GLN* 2.8 39.0 + - - +
35B SER* 3.4 23.0 + - - -
107B PRO* 3.6 9.6 - - - +
108B ALA* 2.8 39.1 + - + +
178B TRP* 3.4 28.0 - - + -
179B LYS 3.1 9.2 - - - +
180B SER* 3.9 24.6 + - - +
191B GLU* 4.5 2.2 + - - +
192B LEU* 1.3 88.7 + - - +
194B ILE* 1.3 62.4 - - - +
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Residues in contact with ILE 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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30B PHE* 3.9 25.4 - - + -
31B GLU 3.2 11.0 - - - +
32B LEU* 4.0 18.6 - - + -
142B PHE* 4.0 22.2 - - + -
144B LEU* 4.3 4.3 - - + -
168B HIS* 5.4 0.4 - - + -
172B ILE* 4.4 12.0 - - + +
177B ARG 4.6 0.2 - - - +
178B TRP* 3.7 2.9 - - - -
179B LYS* 2.9 50.4 + - + +
181B LEU* 3.9 18.8 - - + -
192B LEU* 3.9 20.0 - - + -
193B GLN* 1.3 80.0 - - - +
195B ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 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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30B PHE* 3.7 2.2 - - - -
31B GLU* 2.7 61.6 + - - +
113B ASP* 2.8 30.9 + - - -
172B ILE* 3.9 10.3 - - - -
175B GLU 4.3 9.6 + - - +
176B ASP* 3.1 26.1 + - - +
177B ARG 4.0 14.1 - - - +
178B TRP* 3.3 39.4 - - + +
194B ILE* 1.3 79.4 - - - +
196B VAL* 1.3 70.2 + - - +
197B ARG* 4.0 17.1 - - - +
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Residues in contact with VAL 196 (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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29B TYR 3.3 13.7 - - - +
30B PHE* 3.7 25.1 - - + -
134B PHE* 3.9 21.5 - - + -
138B TRP* 3.8 25.4 - - + +
172B ILE* 4.0 16.2 - - + +
173B ASN 4.6 3.6 + - - +
174B PRO* 3.2 22.4 - - + +
175B GLU 3.0 31.4 + - - +
195B ARG* 1.3 81.7 - - - +
197B ARG* 1.3 68.4 + - - +
207B CYS* 4.9 1.1 - - - -
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Residues in contact with ARG 197 (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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28B GLY* 3.2 2.3 - - - -
29B TYR* 2.9 74.1 + - + +
31B GLU* 2.9 42.1 + - - +
116B ARG* 5.5 4.6 - - - +
131B VAL* 5.3 5.5 - - - +
174B PRO* 4.7 2.5 - - - -
175B GLU 4.9 7.0 - - - +
195B ARG* 4.0 16.5 - - - +
196B VAL* 1.3 75.1 - - - +
198B CYS* 1.3 69.6 + - - +
199B ASP* 5.8 0.4 - - - +
207B CYS* 4.2 4.7 - - - -
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Residues in contact with CYS 198 (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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27B MET 3.6 2.0 - - - +
29B TYR* 5.3 0.7 - - - -
174B PRO* 3.9 10.2 - - - +
197B ARG* 1.3 88.4 + - - +
199B ASP* 1.3 65.8 + - - +
202B TYR 3.4 24.2 - - - +
203B TYR* 4.4 2.7 - - - -
204B SER 3.7 12.6 - - - -
207B CYS* 2.0 57.2 - - + -
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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