Contacts of the strand formed by residues 163 - 168 (chain D) in PDB entry 3F7F
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 PRO 163 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D MET* 3.4 35.4 - - + +
103D ASN* 5.0 0.2 - - - +
107D THR* 5.2 1.1 - - + -
122D ILE* 4.2 15.7 - - + -
158D PHE* 3.3 29.8 - - + -
162D VAL* 1.3 96.5 - - - +
164D HIS* 1.3 65.7 + - - +
165D PHE 5.1 0.2 - - - +
176D VAL* 3.5 30.1 - - + -
177D PHE 3.5 2.9 - - - +
178D LEU* 3.3 13.4 - - + -
179D GLU* 4.2 0.4 - - - -
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Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 2.9 43.5 + - + +
106D TYR* 3.7 5.9 - - - +
107D THR* 3.8 8.9 - - - +
163D PRO* 1.3 76.4 - - - +
165D PHE* 1.3 60.5 + - + +
177D PHE* 2.7 45.8 + - + -
178D LEU 3.7 19.5 - - - -
179D GLU* 3.7 25.1 - - + +
222D SER* 3.8 17.8 + - - -
223D VAL 2.9 28.3 + - - -
224D ILE* 5.6 0.6 - - - +
239D GLN* 5.9 1.1 + - - -
276D VAL* 3.5 26.0 - - + +
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TYR* 3.4 22.7 - + + -
107D THR* 4.5 1.0 - - - +
122D ILE* 5.6 0.8 - - - +
163D PRO* 5.1 0.6 - - - +
164D HIS* 1.3 90.4 - - + +
166D LEU* 1.3 69.7 + - - +
167D PHE* 4.3 12.1 - + - -
176D VAL* 3.7 2.1 - - - -
177D PHE* 2.8 65.1 + + + -
223D VAL* 3.9 15.5 - - + -
225D SER* 4.1 6.1 - - - -
226D CYS* 3.6 40.2 - - + -
276D VAL* 4.1 23.6 - - + -
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TYR 3.0 9.6 + - - +
107D THR* 3.4 36.6 - - - +
108D LEU 4.4 6.1 - - - +
109D THR* 4.0 28.9 - - + -
120D ASN* 4.0 6.1 - - + +
122D ILE* 3.9 21.3 - - + +
128D PHE* 3.9 25.8 - - + -
165D PHE* 1.3 85.2 - - - +
167D PHE* 1.3 64.6 + - - +
168D TYR 4.3 0.2 - - - -
174D SER* 4.2 15.0 - - - +
175D VAL 3.4 19.3 - - - +
176D VAL* 4.1 8.3 - - + +
186D LEU* 5.0 0.4 - - + -
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Residues in contact with PHE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D PHE* 4.0 11.0 + + + -
166D LEU* 1.3 78.8 - - - +
168D TYR* 1.3 89.1 + - - +
169D VAL* 3.7 9.2 - - + -
174D SER* 3.1 16.1 - - - -
175D VAL* 3.1 22.1 + - + -
177D PHE* 4.0 20.0 - - + -
226D CYS* 3.1 38.1 - - + -
227D LYS* 4.0 4.0 - - + -
228D LEU* 3.4 34.1 - - + -
234D LEU* 3.3 24.9 - - + -
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Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D THR* 3.5 26.3 + - + +
111D GLN* 3.4 51.9 - - + +
112D GLU 5.6 0.7 + - - -
113D VAL* 4.7 7.3 - - + +
118D LEU* 5.2 9.6 - - + -
120D ASN* 5.0 10.1 - - - -
166D LEU 4.3 0.6 + - - -
167D PHE* 1.3 100.2 - - - +
169D VAL* 1.3 72.0 + - - +
170D SER* 3.2 32.1 - - - -
171D PRO* 3.0 34.0 - - + +
174D SER* 3.4 10.3 - - - -
228D LEU* 4.9 0.5 - - - +
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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