Contacts of the strand formed by residues 174 - 186 (chain M) in PDB entry 5I2D
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 VAL 174 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44M LEU* 3.5 26.9 - - + +
45M LEU* 4.4 5.5 - - + +
48M ILE* 4.3 11.0 - - + -
172M SER* 3.0 18.7 + - - +
173M PRO* 1.3 78.4 - - + +
175M ARG* 1.3 64.5 + - - +
176M ARG 3.8 5.6 - - - +
177M VAL* 3.6 31.9 - - + -
199M ILE* 4.2 7.0 - - + -
200M TRP 3.5 11.4 - - - +
201M THR* 4.0 8.1 - - + -
210M ALA* 3.9 28.3 - - + -
851O LEU* 4.4 6.9 - - - +
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Residues in contact with ARG 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M GLU* 5.5 2.0 + - - -
45M LEU* 4.6 5.4 - - - +
83M LYS 5.3 3.8 + - - -
84M GLU* 4.1 18.3 + - - +
86M VAL* 3.8 15.8 - - - +
170M VAL* 5.3 11.3 - - - +
172M SER 5.3 2.7 + - - +
173M PRO 3.5 2.2 + - - +
174M VAL* 1.3 75.3 - - - +
176M ARG* 1.3 60.0 + - - +
200M TRP* 2.5 19.1 + - + +
201M THR 3.8 18.4 - - - -
202M ASP* 3.5 30.0 + - - +
845O ASN* 4.7 18.6 + - - +
847O ASP* 4.0 40.0 - - + +
848O GLU* 6.3 0.6 - - - +
851O LEU* 4.7 10.5 - - - +
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Residues in contact with ARG 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M LEU* 4.5 4.0 - - - -
174M VAL* 3.6 1.3 - - - +
175M ARG* 1.3 80.8 - - - +
177M VAL* 1.3 78.3 + - - +
178M ALA* 4.9 7.2 - - + +
198M ARG* 5.8 1.0 - - - +
199M ILE* 3.6 1.4 - - - -
200M TRP* 2.9 85.8 + - + +
847O ASP* 4.4 13.4 + - - +
884O ARG* 3.3 48.0 - - - +
888O GLU* 2.8 32.5 + - - -
937O TYR* 5.9 0.4 + - - -
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Residues in contact with VAL 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M ARG* 3.4 55.1 + - + -
44M LEU* 3.6 25.1 - - + -
45M LEU* 3.9 15.7 - - + +
174M VAL* 3.6 20.4 - - + -
176M ARG* 1.3 87.7 - - - +
178M ALA* 1.3 65.7 + - - +
179M PHE* 5.7 0.4 - - + -
197M LEU* 4.0 22.7 - - + -
198M ARG 3.4 4.5 - - - +
199M ILE* 4.9 2.7 - - + -
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Residues in contact with ALA 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M ARG* 5.3 0.7 - - - +
176M ARG* 4.9 8.1 - - + +
177M VAL* 1.3 76.7 - - - +
179M PHE* 1.3 64.8 + - - +
197M LEU* 3.8 3.8 - - - +
198M ARG* 2.9 55.5 + - + +
200M TRP* 4.1 11.5 - - + -
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Residues in contact with PHE 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M VAL* 4.1 11.2 - - + -
37M GLY* 3.9 29.4 - - - +
38M ASN* 3.1 30.7 - - - -
41M ARG* 4.3 22.7 - - + -
177M VAL* 5.7 0.4 - - + -
178M ALA* 1.3 77.7 - - - +
180M GLN* 1.3 60.1 + - - +
181M VAL* 3.9 27.3 + - + -
195M LEU* 4.2 2.5 - - + -
196M THR 3.2 9.9 - - - +
197M LEU* 4.1 18.6 - - + -
198M ARG* 5.4 1.3 - - - -
979N THR* 5.7 2.2 - - + -
936O TYR* 4.8 6.9 + - - -
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Residues in contact with GLN 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M PHE* 1.3 75.3 - - - +
181M VAL* 1.3 70.5 + - - +
182M GLU* 5.1 13.2 + - + +
194M LYS 3.6 1.9 - - - +
195M LEU* 3.7 1.2 - - - +
196M THR* 2.9 49.0 + - + +
198M ARG* 5.6 10.4 + - - +
638O LYS* 5.8 4.0 - - - +
936O TYR* 4.0 35.4 + - - +
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Residues in contact with VAL 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M GLY* 3.5 44.4 - - - +
34M VAL* 3.7 19.3 - - + +
179M PHE* 3.9 16.7 + - + -
180M GLN* 1.3 80.5 - - - +
182M GLU* 1.3 64.1 + - - +
193M ASP* 4.0 20.4 - - - +
194M LYS 3.4 7.0 - - - +
195M LEU* 4.1 3.4 - - + -
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Residues in contact with GLU 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M GLN* 4.1 13.5 + - + +
181M VAL* 1.3 77.9 - - - +
183M ASP* 1.3 69.7 + - - +
193M ASP* 3.8 3.1 - - - -
194M LYS* 2.9 75.3 + - + +
196M THR* 5.5 3.6 - - - +
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Residues in contact with ASP 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182M GLU* 1.3 84.9 - - - +
184M THR* 1.3 60.7 + - - +
190M THR* 4.1 10.4 - - + +
191M ASP* 3.7 23.1 - - - +
192M LEU 3.2 14.3 - - - +
193M ASP* 4.2 5.6 - - - +
194M LYS* 5.5 0.2 - - - +
851N LYS* 4.7 12.1 + - - -
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Residues in contact with THR 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M GLU* 3.6 15.6 + - - +
27M PRO* 4.2 13.5 - - + -
183M ASP* 1.3 77.5 - - - +
185M ARG* 1.3 69.6 + - - +
190M THR* 3.0 8.1 - - - +
192M LEU* 2.9 54.8 + - + +
193M ASP 4.0 13.5 - - - +
194M LYS* 4.2 15.3 - - + +
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Residues in contact with ARG 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M PRO* 5.9 0.8 - - - +
184M THR* 1.3 84.4 + - - +
186M LEU* 1.3 57.9 + - - +
187M GLY* 3.7 28.5 + - - +
189M ARG 3.1 17.5 - - - +
190M THR* 3.6 25.1 + - + -
192M LEU* 4.6 3.4 - - - -
688O TRP* 5.4 7.7 - - - +
689O ASP* 2.9 27.7 + - - +
692O GLU* 3.9 35.2 + - - +
51P LEU* 4.8 10.0 - - - +
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Residues in contact with LEU 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LYS* 4.7 30.3 - - + +
27M PRO* 4.5 14.8 - - + -
185M ARG* 1.3 71.2 - - - +
187M GLY* 1.3 57.8 + - - +
188M GLN* 2.8 28.6 + - - +
189M ARG* 3.0 21.1 + - + +
192M LEU* 3.7 24.9 - - + +
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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