Contacts of the strand formed by residues 180 - 184 (chain M) in PDB entry 3HOU
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 LYS 180 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M PHE* 4.9 1.6 - - + -
96M ILE* 6.3 0.2 - - - -
176M LYS* 3.7 5.0 - - - +
177M ASP* 2.6 57.7 + - + +
178M GLY 3.2 0.6 + - - -
179M LEU* 1.3 84.3 - - + +
181M LEU* 1.3 63.6 + - - +
182M VAL* 6.0 1.6 - - + -
201M VAL* 4.6 21.5 - - + -
202M LEU 6.0 0.9 - - - +
290M GLU* 4.7 5.1 + - - +
293M GLU* 5.2 4.8 + - - +
294M SER* 3.4 39.1 - - - +
297M GLN* 5.3 8.1 - - + +
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Residues in contact with LEU 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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91M PHE* 4.1 31.6 - - + -
96M ILE* 4.8 8.7 - - + +
99M ILE* 4.4 9.9 - - + -
100M LYS* 3.7 54.7 - - + +
103M CYS* 4.9 4.3 - - + -
174M ILE* 4.2 6.5 - - + -
175M ARG 3.9 4.5 - - - +
176M LYS* 4.5 10.3 - - + -
180M LYS* 1.3 78.2 - - - +
182M VAL* 1.3 60.6 + - - +
201M VAL* 3.8 3.8 - - - +
202M LEU* 2.8 46.8 + - + +
207M ILE* 4.5 11.2 - - + -
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Residues in contact with VAL 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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173M THR 3.8 0.5 - - - +
174M ILE* 3.3 6.0 - - - +
175M ARG* 2.8 65.1 + - + +
177M ASP* 5.3 9.9 - - + -
180M LYS* 4.0 3.3 + - + +
181M LEU* 1.3 73.9 - - - +
183M GLY* 1.3 64.8 + - - +
199M LEU* 5.0 10.8 - - + -
200M ARG* 3.5 8.1 - - - +
201M VAL* 3.4 40.4 - - + +
202M LEU* 4.6 0.9 - - - -
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Residues in contact with GLY 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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172M PRO* 4.1 8.5 - - - -
173M THR 3.2 11.7 - - - -
174M ILE* 4.2 3.1 - - - -
175M ARG* 6.3 0.2 - - - -
182M VAL* 1.3 77.8 - - - +
184M SER* 1.3 61.2 + - - -
185M TRP* 3.1 13.8 - - - -
199M LEU* 3.5 3.3 - - - +
200M ARG 3.0 35.6 + - - +
202M LEU* 4.5 4.5 - - - +
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Residues in contact with SER 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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171M GLN 5.0 0.2 - - - +
173M THR* 3.1 41.3 + - - +
175M ARG* 4.6 5.6 + - - -
183M GLY* 1.3 70.5 - - - -
185M TRP* 1.3 66.3 + - - +
186M LYS* 3.2 8.5 + - - +
197M PRO* 4.0 17.8 - - - +
198M GLU 4.6 0.7 - - - -
199M LEU* 3.3 36.0 - - - +
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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