Contacts of the strand formed by residues 163 - 167 (chain L) in PDB entry 5FHX
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 163 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H ASP 6.0 0.2 - - - -
113H TRP* 5.2 0.9 - - - -
154L PHE* 3.2 5.2 - - - -
155L GLN* 2.9 47.3 + - + +
161L ILE* 4.4 4.9 - - + +
162L PRO* 1.3 74.3 - - - +
164L LEU* 1.3 74.1 + - - +
165L LEU* 3.5 6.4 + - + +
175L GLY 5.1 7.3 + - - -
176L VAL* 4.6 15.0 - - - +
177L PRO* 5.8 0.8 - - - +
401L PO4 3.0 31.2 + - - +
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Residues in contact with LEU 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H TYR* 3.4 39.9 - - + -
110H PHE 3.8 14.8 + - - +
111H ASP* 4.3 11.6 + - - +
113H TRP* 5.0 1.0 - - - +
152L SER* 3.8 16.2 - - - +
153L TRP 4.2 0.7 - - - +
154L PHE* 3.6 29.0 - - + -
163L LYS* 1.3 80.1 - - - +
165L LEU* 1.3 60.3 + - - +
166L ILE 3.7 21.8 - - - +
167L TYR* 4.5 5.2 - - + -
173L HIS* 3.6 38.4 + - + +
176L VAL* 3.6 14.7 - - - +
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Residues in contact with LEU 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L TRP* 2.8 17.8 + - + +
154L PHE 4.3 2.7 - - - -
155L GLN* 4.0 25.6 - - + +
163L LYS* 4.1 6.1 - - - +
164L LEU* 1.3 79.1 - - - +
166L ILE* 1.3 71.0 + - + +
172L LEU* 3.6 1.7 - - - -
173L HIS* 2.9 27.1 + - - +
176L VAL* 3.7 32.3 - - + +
180L PHE* 3.8 20.2 - - + -
191L LEU* 4.4 9.2 - - + -
204L TYR* 3.5 35.9 - - + -
401L PO4 4.4 13.7 - - - +
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Residues in contact with ILE 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L LEU 4.7 0.2 - - - +
152L SER* 3.1 5.2 - - - -
153L TRP* 2.7 42.5 + - + +
164L LEU* 3.7 4.5 - - - +
165L LEU* 1.3 86.3 - - + +
167L TYR* 1.3 64.4 + - - +
169L ALA* 3.5 32.8 - - - +
170L SER 3.7 4.0 - - - +
171L ASN 3.2 13.7 - - - +
172L LEU* 3.8 17.5 - - + -
173L HIS 4.6 0.2 - - - +
180L PHE* 4.4 1.1 - - + -
181L SER* 3.5 15.9 - - - +
182L GLY* 3.4 28.0 - - - +
191L LEU* 3.8 17.9 - - + -
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Residues in contact with TYR 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H SER* 3.9 17.7 + - - -
108H PHE 5.6 0.4 - - - +
109H TYR* 3.6 62.5 + + + -
151L LEU 3.9 1.3 - - - -
152L SER* 3.8 7.4 - - - +
164L LEU* 4.5 6.3 - - + -
166L ILE* 1.3 74.1 - - - +
168L LYS* 1.3 74.5 + - + +
169L ALA 3.3 2.2 - - - -
171L ASN* 2.9 59.2 + - + +
172L LEU 3.8 20.5 + - - -
173L HIS* 4.4 13.5 - + - -
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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