Contacts of the strand formed by residues 175 - 178 (chain I) in PDB entry 3STJ
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 PHE 175 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I LEU* 3.7 1.4 - - - -
163I GLY 3.2 9.8 + - - -
164I ARG* 2.9 42.9 + - + +
167I LEU* 3.7 18.8 - - + -
169I LEU* 4.0 19.1 - - + -
170I GLU* 4.1 24.5 - - + -
172I LEU 5.3 0.9 - - - -
173I GLU* 3.7 33.2 - - + -
174I ASN* 1.3 78.6 - - - +
176I ILE* 1.3 61.2 + - - +
203I THR* 3.9 24.7 - - + -
204I ALA* 5.0 1.1 - - + -
217I PHE* 3.7 28.7 - - + -
218I ALA 3.4 20.4 - - - +
219I ILE* 3.9 14.8 - - + -
220I PRO* 5.3 0.2 - - + -
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Residues in contact with ILE 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I SER* 5.4 0.2 - - - -
135I LEU* 3.7 13.9 - - + -
159I VAL* 4.1 21.1 - - + -
161I ALA 3.7 8.7 - - - +
162I LEU* 3.9 15.9 - - + -
163I GLY 5.9 0.2 - - - +
174I ASN 5.0 0.4 - - - +
175I PHE* 1.3 74.3 - - - +
177I GLN* 1.3 69.4 + - - +
178I THR* 4.2 1.1 + - - +
191I LEU* 4.0 20.4 - - + -
199I ILE 3.2 30.5 - - - +
200I GLY* 4.5 2.9 - - - -
216I GLY 3.6 0.3 - - - +
217I PHE* 3.3 5.9 - - - -
218I ALA* 2.9 37.3 + - + +
220I PRO* 3.6 26.5 - - + -
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Residues in contact with GLN 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H LEU* 3.9 5.1 - - - +
153H THR* 3.1 36.8 + - - +
159I VAL* 3.6 3.8 - - - -
160I SER* 2.7 32.2 + - - -
161I ALA* 2.9 26.2 + - + +
164I ARG* 2.9 35.5 + - + -
175I PHE 4.0 0.2 + - - -
176I ILE* 1.3 76.4 - - - +
178I THR* 1.3 59.9 + - - +
214I GLY 5.2 0.6 + - - -
215I ILE* 3.9 25.1 - - + +
216I GLY 3.2 8.1 - - - +
217I PHE* 3.5 27.7 - - + -
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Residues in contact with THR 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I ALA* 4.2 7.6 - - - +
158I ILE 2.9 21.6 + - - -
159I VAL* 4.9 1.6 - - - -
160I SER* 3.8 5.8 - - - -
176I ILE 5.2 1.6 - - - +
177I GLN* 1.3 76.7 - - - +
179I ASP* 1.3 59.2 + - - +
180I ALA* 3.2 18.3 + - + +
182I ILE* 3.5 30.1 - - + -
191I LEU* 3.9 28.0 - - + -
202I ASN* 4.7 1.1 - - - +
214I GLY 3.3 3.4 - - - +
215I ILE* 4.1 0.3 - - - -
216I GLY* 2.9 37.3 + - - +
217I PHE* 5.5 0.9 - - - -
218I ALA* 5.6 0.4 - - + -
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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