Contacts of the strand formed by residues 170 - 175 (chain H) in PDB entry 2E9X
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 TYR 170 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F PHE* 5.0 2.2 - + - -
140F GLU 4.5 3.1 + - - -
141F ALA* 3.6 42.9 - - - +
161F THR* 3.2 32.5 - - + +
164F LEU* 3.5 47.8 - - + -
165F ASN* 2.8 24.3 + - - +
168F TYR* 4.2 22.2 - - + +
168H ASP 4.7 0.9 - - - -
169H SER* 1.3 73.9 - - - +
171H VAL* 1.3 65.7 + - - +
186H PRO 4.2 2.3 + - - -
205H LEU* 4.2 6.7 - - + -
206H ILE* 3.5 21.1 - - - -
207H ARG* 3.6 27.4 - - + +
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Residues in contact with VAL 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F THR* 4.4 3.6 - - - -
39H PHE* 3.7 31.4 - - + +
41H PRO* 4.7 2.2 - - + -
169H SER* 3.9 9.0 - - - +
170H TYR* 1.3 79.7 - - - +
172H PHE* 1.3 66.8 + - - +
173H LEU* 5.1 0.9 - - + -
204H HIS 3.8 0.3 - - - +
205H LEU* 3.4 6.5 - - - +
206H ILE* 3.0 38.6 + - + +
208H TYR* 4.0 24.0 - - + -
211H ILE* 4.3 6.5 - - + -
222H LEU* 3.7 27.1 - - + -
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Residues in contact with PHE 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F LEU* 3.7 33.2 - - + -
148F LEU* 5.9 1.6 - - + -
153F ILE* 3.7 24.0 - - + -
157F GLY* 3.9 21.5 - - - -
160F LEU* 4.5 19.5 - - + -
161F THR* 3.9 23.6 - - + -
39H PHE* 6.0 0.4 - - - +
171H VAL* 1.3 77.8 - - - +
173H LEU* 1.3 65.0 + - - +
204H HIS 3.1 11.9 - - - -
205H LEU* 4.1 27.8 - - + -
222H LEU* 3.4 10.4 - - - +
223H ILE* 3.1 45.6 + - + +
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Residues in contact with LEU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H VAL* 5.1 0.7 - - + -
172H PHE* 1.3 77.9 - - - +
174H ARG* 1.3 63.9 + - - +
175H VAL* 3.7 27.4 - - + -
198H LEU* 4.8 4.3 - - + -
203H GLN* 3.0 7.3 - - - +
204H HIS* 2.8 50.8 + - + +
206H ILE* 4.0 27.4 - - + -
211H ILE* 4.0 27.4 - - + -
220H VAL* 4.1 17.0 - - + -
221H GLN 3.3 13.9 - - - +
222H LEU* 4.0 9.0 - - + -
223H ILE* 3.7 8.0 - - - +
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Residues in contact with ARG 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H GLU* 4.7 6.5 + - - -
32H GLN* 5.8 0.6 - - - +
173H LEU* 1.3 77.6 - - - +
175H VAL* 1.3 63.7 + - - +
176H ARG* 3.8 12.4 + - - +
201H GLY 5.4 3.4 - - - +
202H SER 3.0 9.2 - - - +
203H GLN* 4.3 16.4 - - + +
220H VAL* 3.5 1.4 - - - -
221H GLN* 2.8 73.8 + - + +
223H ILE* 4.0 17.2 - - + +
1004H SO4 2.9 43.3 + - - -
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Residues in contact with VAL 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H LEU* 3.7 19.7 - - + -
174H ARG* 1.3 75.9 + - - +
176H ARG* 1.3 57.6 + - - +
177H GLU 3.3 31.4 - - - +
179H GLN* 5.0 0.2 - - + -
198H LEU* 3.6 32.3 - - + +
199H GLU 3.3 19.7 - - - +
200H LYS* 4.1 0.2 - - - -
201H GLY* 2.7 29.3 + - - -
202H SER* 2.9 26.9 + - - +
204H HIS* 4.0 2.7 - - + -
219H ALA 4.0 5.6 - - - +
220H VAL* 4.2 5.4 - - + -
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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