Contacts of the strand formed by residues 189 - 198 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ALA* 3.7 3.7 + - + +
37D LEU* 3.3 5.5 - - - -
38D ARG* 3.0 66.5 + - + +
182D HIS* 4.9 5.2 - - + +
183D PHE 3.3 22.4 - - - +
184D SER* 3.4 22.9 - - - -
188D ALA* 1.3 76.1 - - - +
190D LEU* 1.3 62.1 + - - +
191D GLU* 3.3 44.3 + - + +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.8 6.3 - - + -
36D ALA 3.3 4.5 - - - +
37D LEU* 3.4 40.4 - - + -
146D VAL* 4.9 16.6 - - + +
148D ALA* 5.3 6.3 - - + +
164D GLU* 5.0 7.0 - - + +
166D VAL* 3.6 38.1 - - + -
181D LEU 4.1 0.4 - - - +
182D HIS* 3.5 0.5 - - - -
183D PHE* 2.8 44.3 + - + +
188D ALA* 4.4 12.1 - - + +
189D HIS* 1.3 78.9 + - - +
191D GLU* 1.3 70.4 + - - +
192D LEU* 4.7 9.0 - - + -
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Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.7 2.0 - - - +
35D SER* 2.6 41.3 + - - +
36D ALA* 3.0 26.3 + - + +
38D ARG* 5.7 0.2 + - - -
104D TYR* 5.7 0.9 - - - -
181D LEU 3.4 5.8 - - - +
182D HIS* 2.4 41.6 + - + +
189D HIS* 3.3 29.2 + - + +
190D LEU* 1.3 81.1 - - - +
192D LEU* 1.3 60.0 + - - +
193D GLN* 4.3 2.5 - - - +
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Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 4.1 17.7 - - + -
33D GLN 3.2 15.7 - - - +
34D LEU* 3.9 13.9 - - + -
144D LEU* 4.3 4.7 - - + -
146D VAL* 4.3 25.1 - - + -
181D LEU* 2.8 57.5 + - + +
183D PHE* 4.2 22.2 - - + -
190D LEU* 4.7 11.0 - - + -
191D GLU* 1.3 76.5 - - - +
193D GLN* 1.3 72.4 + - - +
194D ILE* 3.9 14.6 - - + -
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.3 3.3 - - - +
33D GLN* 2.7 51.2 + - - +
35D SER* 3.4 20.9 + - - -
107D PRO* 3.8 9.3 - - - +
108D ALA* 3.3 31.7 + - + +
178D TRP* 3.4 26.5 - - + -
179D LYS 3.3 7.9 - - - +
180D SER* 3.5 26.4 + - - +
182D HIS* 6.1 2.4 - - - -
191D GLU* 4.3 2.4 - - - +
192D LEU* 1.3 89.3 + - - +
194D ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PHE* 3.9 20.4 - - + -
31D GLU 3.2 13.7 - - - +
32D LEU* 3.9 17.3 - - + -
142D PHE* 3.8 30.5 - - + -
144D LEU* 4.1 7.4 - - + -
168D HIS* 5.1 2.9 - - + -
172D ILE* 3.9 12.9 - - + +
177D ARG 3.5 0.9 - - - +
178D TRP* 3.3 4.5 - - - -
179D LYS* 2.8 41.8 + - + +
181D LEU* 3.7 17.7 - - + -
192D LEU* 3.9 12.1 - - + -
193D GLN* 1.3 80.2 - - - +
195D ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 195 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D PHE* 3.8 2.4 - - - -
31D GLU* 3.0 63.3 + - + +
172D ILE* 3.7 11.4 - - - -
177D ARG* 3.4 22.2 - - - +
178D TRP* 3.4 44.9 - - + +
194D ILE* 1.3 78.5 - - - +
196D VAL* 1.3 72.2 + - - +
197D ARG* 4.0 25.0 - - - +
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D TYR 3.6 13.5 - - - +
30D PHE* 3.6 32.3 - - + -
134D PHE* 4.2 13.5 - - + -
138D TRP* 3.9 31.2 - - + +
172D ILE* 4.3 11.8 - - + +
173D ASN 5.0 1.9 + - - -
174D PRO* 3.2 51.3 - - + +
177D ARG* 4.9 1.5 + - - +
195D ARG* 1.3 76.8 - - - +
197D ARG* 1.3 67.2 + - - +
207D CYS* 4.7 2.5 - - - -
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Residues in contact with ARG 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLY* 3.5 2.1 - - - -
29D TYR* 3.2 78.5 + - + +
31D GLU* 3.6 23.6 + - - +
131D VAL* 5.3 2.6 - - - +
174D PRO* 4.8 3.1 - - - -
195D ARG* 4.0 28.8 - - - +
196D VAL* 1.3 76.1 - - - +
198D CYS* 1.3 79.3 + - - +
199D ASP* 4.5 1.0 - - - +
207D CYS* 3.8 6.9 - - - -
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Residues in contact with CYS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET 4.1 0.2 - - - -
174D PRO* 4.6 7.4 - - - +
197D ARG* 1.3 91.0 + - - +
199D ASP* 1.3 67.6 + - - +
202D TYR* 3.5 25.8 - - + +
203D TYR* 4.3 2.9 - - - -
204D SER 3.9 13.5 - - - -
207D CYS* 2.0 53.8 - - + -
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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