Contacts of the strand formed by residues 104 - 108 (chain F) in PDB entry 1K9A
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 PHE 104 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TRP* 3.8 27.0 - + + +
96F LEU* 6.0 1.3 - - - -
102F GLY 3.3 17.5 - - - -
103F LEU* 1.3 82.0 - - - +
105F LEU* 1.3 68.3 + - - +
106F VAL* 4.8 4.3 - - + -
118F LEU* 4.6 2.9 - - + -
119F CYS 3.0 15.7 - - - +
120F VAL* 3.5 13.2 - - + -
153F VAL* 3.4 35.7 - - + -
157F THR* 4.9 1.1 - - - -
167F LEU* 3.5 32.1 - - + -
168F ILE 3.9 17.7 - - - -
169F LYS 3.4 9.3 + - - -
170F PRO* 4.1 13.7 - - + -
171F LYS* 3.0 26.7 + - - +
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Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F TRP* 4.0 5.8 - - - -
84F HIS* 3.5 22.4 - - + +
87F ILE* 5.5 0.9 - - + -
92F ALA* 3.8 35.4 - - + +
95F LEU* 4.5 6.5 - - + -
96F LEU* 3.9 13.2 - - + -
104F PHE* 1.3 79.1 - - - +
106F VAL* 1.3 67.5 + - - +
107F ARG* 3.8 13.0 - - + +
118F LEU* 3.7 1.9 - - - +
119F CYS* 2.8 56.3 + - + +
171F LYS* 3.5 27.1 - - + -
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F TRP* 3.6 38.8 + - + -
83F PHE* 3.7 5.4 - - + -
84F HIS* 3.1 23.6 + - - -
104F PHE* 4.8 3.1 - - + -
105F LEU* 1.3 81.9 - - - +
107F ARG* 1.3 69.1 + - - +
116F TYR* 4.3 0.2 - - + -
117F THR 3.0 22.4 - - - +
118F LEU* 4.5 12.6 - - + -
131F ILE* 4.2 7.6 - - + -
149F LEU* 3.6 28.0 - - + -
153F VAL* 4.4 11.0 - - + -
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PHE* 3.9 9.5 - - - -
84F HIS* 4.4 8.5 - - - -
85F GLY 4.5 5.6 - - - +
87F ILE* 3.2 33.3 + - + +
89F ARG* 3.1 32.1 - - - +
92F ALA* 4.1 8.1 - - - -
105F LEU* 3.8 9.4 - - + +
106F VAL* 1.3 88.1 - - - +
108F GLU* 1.3 94.0 + - - +
110F THR* 3.4 10.1 + - - -
111F ASN* 2.6 32.7 + - - +
116F TYR* 3.9 1.6 - - - -
117F THR* 2.9 45.5 + - + +
119F CYS* 3.7 18.2 - - - -
128F HIS* 5.1 10.5 + - - +
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Residues in contact with GLU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PHE* 4.6 4.2 - - + -
85F GLY* 2.7 33.9 + - - +
86F LYS* 4.2 17.2 - - + +
107F ARG* 1.3 89.5 + - - +
109F SER* 1.3 61.4 + - - +
110F THR* 2.6 34.7 + - - +
114F GLY 6.2 0.2 - - - +
115F ASP 3.7 10.8 - - - +
116F TYR* 3.9 27.3 + - + +
117F THR 4.3 0.4 - - - -
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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