Contacts of the strand formed by residues 156 - 160 (chain C) in PDB entry 3D7S
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 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASN 6.1 0.2 - - - -
155C LEU* 1.3 73.4 - - - +
157C VAL* 1.3 60.0 + - - +
183C ARG* 3.4 32.7 - - + +
185C TYR* 2.6 29.5 + - + -
221C GLU* 3.2 28.2 - - + +
222C VAL* 3.9 2.8 - - - -
223C ASP* 3.0 41.9 + - - +
224C ILE 3.1 8.3 + - - +
258C LYS* 4.1 8.3 - - - -
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 5.7 2.9 - - + -
155C LEU* 4.4 20.4 - - + +
156C HIS* 1.3 76.2 - - - +
158C ALA* 1.3 66.1 + - - +
159C MET* 3.7 28.3 - - + +
172C LEU* 5.1 1.1 - - + -
176C LEU* 4.4 14.8 - - + -
182C ASN* 5.2 2.7 - - - +
183C ARG 3.0 7.7 + - - +
184C PHE* 3.5 26.5 - - + +
185C TYR* 2.8 30.6 + - - +
222C VAL* 5.3 0.2 - - - -
224C ILE* 3.5 30.7 - - + -
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C VAL* 1.3 74.8 - - - +
159C MET* 1.3 65.6 + - - +
160C VAL* 4.7 3.6 - - + -
185C TYR* 3.3 11.4 - - + +
187C ILE* 5.0 1.6 - - + -
215C ILE* 6.4 0.4 - - + -
218C VAL* 4.9 6.1 - - + -
222C VAL* 4.0 20.0 - - + -
224C ILE 2.6 18.1 + - - +
225C LEU* 3.9 20.2 - - + -
226C TYR* 2.7 30.2 + - - +
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Residues in contact with MET 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C VAL* 3.7 21.5 - - + +
158C ALA* 1.3 78.9 - - - +
160C VAL* 1.3 61.1 + - - +
163C LEU* 3.3 19.7 - - + +
169C VAL* 3.6 22.4 - - + -
172C LEU* 3.2 36.8 - - + -
173C THR* 3.3 26.9 - - - +
176C LEU* 3.9 7.4 - - + -
184C PHE* 4.9 2.5 - - + -
185C TYR 2.7 9.4 + - - +
186C PHE* 3.5 26.0 - - + -
187C ILE 3.2 21.7 + - - -
226C TYR* 3.6 12.3 - - + +
228C THR* 5.9 0.2 - - - -
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ALA* 4.7 2.2 - - + -
159C MET* 1.3 79.7 - - - +
161C GLY* 1.3 62.4 + - - +
163C LEU* 3.7 3.1 - - - +
187C ILE* 3.5 17.5 - - + +
215C ILE* 3.8 26.5 - - + -
225C LEU* 3.3 34.3 - - + -
226C TYR 2.9 8.4 + - - +
227C MET* 3.5 24.9 - - + +
228C THR* 2.9 32.8 + - - +
247C PHE* 4.1 17.7 - - + +
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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