Contacts of the strand formed by residues 172 - 175 (chain C) in PDB entry 3SRF
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 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLY 4.1 6.1 - - - +
171C SER* 1.3 73.5 - - - +
173C ILE* 1.3 63.1 + - - +
174C TYR* 3.6 34.7 + - + +
181C SER* 4.6 3.6 + - - +
182C LEU 3.3 10.5 - - - +
183C GLN* 3.5 28.0 - - - +
197C GLU* 3.2 24.0 + - - +
209C ASN 4.3 0.5 - - - +
210C LEU* 4.4 3.8 - - - +
211C PRO* 3.7 28.0 + - + +
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Residues in contact with ILE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 4.0 15.5 - - + -
158C LEU* 5.5 3.1 - - + -
163C ILE* 4.8 3.4 - - + -
167C VAL* 4.5 6.5 - - + -
171C SER 4.7 0.4 - - - +
172C LYS* 1.3 74.8 - - - +
174C TYR* 1.3 64.7 + - - +
175C VAL* 4.4 2.5 - - + -
181C SER* 3.7 0.7 - - - -
182C LEU* 2.8 61.9 + - + +
184C VAL* 3.7 29.6 - - + -
192C LEU* 3.9 21.8 - - + -
194C THR* 4.3 1.8 - - + -
208C VAL* 3.9 24.9 - - + -
209C ASN 3.8 2.9 - - - -
210C LEU* 3.6 20.2 - - + -
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LYS* 3.6 37.1 + - + +
173C ILE* 1.3 75.0 - - - +
175C VAL* 1.3 60.8 + - - +
178C GLY* 3.9 21.3 - - - -
180C ILE 3.4 3.8 - - - +
181C SER* 3.3 31.3 + - - -
207C GLY 4.5 0.2 - - - -
208C VAL* 3.3 7.6 - - - +
209C ASN* 2.7 39.5 + - + +
211C PRO* 3.7 33.2 - - + -
298C ILE* 3.8 23.8 - - + -
338D ARG* 3.8 20.0 - - - -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C THR* 4.1 15.3 - - + -
156C LEU* 4.6 11.0 - - + -
158C LEU* 5.7 0.9 - - + -
173C ILE* 4.4 6.5 - - + -
174C TYR* 1.3 79.6 - - - +
176C ASP* 1.3 77.2 + - + +
177C ASP 3.9 0.7 - - - -
178C GLY 4.3 1.3 - - - -
179C LEU 3.6 1.4 + - - -
180C ILE* 2.9 40.3 + - + +
182C LEU* 4.1 25.8 - - + -
202C LEU* 3.9 27.8 - - + -
206C LYS* 4.2 8.1 - - + -
207C GLY 3.4 4.9 - - - +
208C VAL* 4.4 10.1 - - + -
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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
------------------------------------------------------------
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