Contacts of the strand formed by residues 173 - 176 (chain D) in PDB entry 3G2G
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 173 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D GLY 3.8 2.8 + - - +
172D SER* 1.3 75.6 - - - +
174D ILE* 1.3 66.9 + - - +
175D TYR* 4.1 26.2 - - + +
182D SER* 5.9 1.1 - - - -
183D LEU 3.1 11.2 - - - +
184D GLN* 4.5 2.9 - - + +
211D LEU* 4.3 7.1 - - - +
212D PRO* 3.9 19.3 + - + +
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ILE* 5.5 5.2 - - + -
159D LEU* 5.5 5.8 - - + -
164D ILE* 5.0 5.8 - - + -
168D VAL* 6.1 2.7 - - + -
172D SER* 4.7 8.1 - - - +
173D LYS* 1.3 81.2 - - - +
175D TYR* 1.3 67.6 + - - +
176D VAL* 4.8 2.5 - - + -
181D ILE 3.9 0.2 - - - +
182D SER* 3.4 2.4 - - - -
183D LEU* 2.7 59.9 + - + +
185D VAL* 5.4 4.9 - - + +
193D LEU* 4.6 18.4 - - + -
195D THR* 4.5 21.3 - - + -
209D VAL* 3.5 26.7 - - + -
210D ASN 3.6 3.8 - - - -
211D LEU* 3.7 17.0 - - + -
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LYS* 4.1 23.3 - - + +
174D ILE* 1.3 73.2 - - - +
176D VAL* 1.3 67.4 + - - +
179D GLY* 3.6 33.9 - - - +
181D ILE 3.3 3.4 - - - -
182D SER* 3.4 29.7 - - - -
208D GLY 4.3 0.4 - - - -
209D VAL* 3.1 9.4 - - - +
210D ASN* 3.0 31.1 + - + +
212D PRO* 3.5 37.9 - - + -
299D ILE* 3.9 18.8 - - + -
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D THR* 4.3 11.9 - - + -
157D LEU* 4.9 10.1 - - + -
174D ILE* 4.8 5.2 - - + +
175D TYR* 1.3 82.3 - - - +
177D ASP* 1.3 78.4 + - + +
179D GLY 3.9 1.6 - - - -
180D LEU 3.3 1.2 + - - -
181D ILE* 2.8 45.0 + - + +
183D LEU* 4.6 17.5 - - + -
203D LEU* 3.9 21.5 - - + -
207D LYS* 3.7 20.4 - - + -
208D GLY 3.3 5.6 - - - +
209D VAL* 4.2 9.6 - - + -
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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