Contacts of the helix formed by residues 138 - 143 (chain V) in PDB entry 3FKS
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 ILE 138 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136V THR* 3.6 8.0 + - - +
137V GLY* 1.3 75.1 - - - +
139V LYS* 1.3 62.9 + - - +
140V VAL* 3.9 13.0 - - + +
141V VAL* 3.5 30.1 - - + -
142V ASP* 2.9 31.0 + - - +
166V PHE* 3.7 31.2 - - + -
169V GLU* 5.4 5.6 - - + -
170V LEU* 4.9 13.7 - - + -
173V ASN* 6.1 1.6 - - - +
346V PRO* 4.6 4.5 - - + -
416V GLN* 3.6 12.1 - - + +
418V PHE* 3.4 39.5 - - + -
437V THR* 5.4 0.3 + - - -
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Residues in contact with LYS 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138V ILE* 1.3 72.1 - - - +
140V VAL* 1.3 61.2 + - - +
141V VAL 3.1 5.1 + - - -
142V ASP* 5.1 0.2 - - - -
143V LEU* 3.1 33.0 + - - +
413V PHE* 3.2 53.7 + - + +
415V SER 3.8 6.2 + - - -
416V GLN* 3.7 23.5 + - + +
432V VAL* 3.5 23.1 - - + -
437V THR* 3.7 30.2 - - + +
441V PHE* 4.4 9.9 - - + -
460V VAL* 3.7 10.3 + - - +
461V GLY 2.9 29.0 + - - +
462V GLY* 4.7 1.6 - - - -
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Residues in contact with VAL 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138V ILE* 3.9 9.2 - - + +
139V LYS* 1.3 77.5 - - - +
141V VAL* 1.3 73.3 + - + +
143V LEU* 4.7 2.5 - - - -
144V LEU* 3.7 25.0 - - + +
346V PRO* 4.3 16.2 - - + -
349V ASP 4.9 7.6 - - - +
350V PRO* 3.9 37.5 - - + +
353V SER* 4.9 5.5 + - - -
413V PHE 5.7 5.2 - - - +
415V SER* 6.3 2.5 - - - +
441V PHE* 6.1 1.8 - - - -
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Residues in contact with VAL 141 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136V THR* 5.0 3.1 - - + +
138V ILE* 3.5 39.2 + - + -
139V LYS 3.1 0.4 - - - -
140V VAL* 1.3 91.6 - - + +
142V ASP* 1.3 62.6 + - - +
143V LEU 3.4 1.3 - - - -
145V ALA* 2.9 31.5 + - + +
147V TYR* 3.7 30.5 - - + +
166V PHE* 4.2 11.7 - - + -
170V LEU* 6.4 0.9 - - + -
332V THR 5.4 0.7 - - - +
333V THR* 3.9 23.1 - - - +
346V PRO* 5.1 1.1 - - + -
353V SER* 5.1 6.3 - - - +
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Residues in contact with ASP 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134V LEU 3.0 22.0 - - - +
135V GLU* 4.1 4.2 - - - -
136V THR* 3.1 31.6 + - - +
137V GLY 4.1 3.1 + - - +
138V ILE 2.9 21.3 + - - +
139V LYS* 5.1 0.4 - - - -
141V VAL* 1.3 77.8 - - - +
143V LEU* 1.3 66.1 + - - +
145V ALA 4.5 1.6 - - - -
146V PRO* 4.0 19.9 - - - +
147V TYR* 5.5 0.7 + - - -
367V HIS* 4.7 3.9 + - - -
433V ARG 4.0 16.5 - - - +
434V LEU* 4.5 18.1 - - - +
437V THR* 5.8 2.5 - - - +
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Residues in contact with LEU 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139V LYS 3.1 20.6 + - - +
140V VAL* 5.9 1.1 - - - -
142V ASP* 1.3 80.9 - - - +
144V LEU* 1.3 73.1 + - + +
145V ALA 3.3 0.3 + - - -
146V PRO* 3.9 5.5 - - - +
358V LEU* 4.4 4.0 - - - +
367V HIS* 3.1 56.1 - - + +
370V VAL* 4.4 18.6 - - + -
371V ALA* 3.6 30.7 - - + +
374V VAL* 4.8 11.7 - - + -
437V THR* 4.5 25.5 - - + +
441V PHE* 5.0 12.6 - - + -
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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
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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