Contacts of the helix formed by residues 138 - 145 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136O THR* 3.4 29.6 + - - +
137O GLY* 1.3 73.9 - - - +
139O LYS* 1.3 61.2 + - - +
140O VAL* 3.6 21.1 - - + +
141O VAL* 3.7 21.8 - - + +
142O ASP* 3.0 32.9 + - - -
166O PHE* 4.4 20.0 - - + -
169O GLU* 4.8 3.6 - - + -
170O LEU* 4.2 18.2 - - + -
173O ASN* 4.5 8.1 - - - +
346O PRO* 4.8 4.0 - - + -
414O LEU 5.5 0.4 - - - +
416O GLN* 3.2 9.8 - - + +
418O PHE* 3.7 31.2 - - + -
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Residues in contact with LYS 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137O GLY 4.2 0.4 - - - -
138O ILE* 1.3 70.2 - - - +
140O VAL* 1.3 68.2 + - - +
142O ASP* 4.0 1.3 - - - +
143O LEU* 3.4 23.6 + - - +
413O PHE* 2.8 42.8 + - + +
414O LEU* 4.0 8.0 - - - +
415O SER 2.9 17.5 + - - -
416O GLN* 2.7 26.7 + - - +
432O VAL* 3.8 25.8 - - + -
437O THR* 4.0 20.1 - - + +
441O PHE* 4.6 7.8 - - + -
460O VAL* 2.8 27.0 + - - +
461O GLY 2.9 20.6 + - - +
462O GLY* 4.8 0.4 - - - -
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Residues in contact with VAL 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O ILE* 3.4 11.4 - - + -
139O LYS* 1.3 76.0 - - - +
141O VAL* 1.3 58.0 + - + +
144O LEU* 2.9 56.4 + - + +
145O ALA* 5.4 0.2 - - - +
333O THR* 6.5 0.2 - - + -
346O PRO* 4.8 12.3 - - + +
348O VAL* 4.0 32.3 - - + +
350O PRO* 4.7 4.7 - - + -
353O SER* 6.3 0.7 - - - -
414O LEU* 3.1 53.6 - - + +
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Residues in contact with VAL 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O THR* 3.8 22.7 - - + +
138O ILE* 3.6 19.8 + - + +
139O LYS 3.4 0.4 - - - -
140O VAL* 1.3 74.4 - - + +
142O ASP* 1.3 65.6 + - - +
143O LEU 2.8 6.6 + - - -
145O ALA* 2.9 50.1 + - - +
146O PRO* 3.0 2.8 - - + -
147O TYR* 3.8 24.7 - - + +
166O PHE* 3.8 19.1 - - + -
333O THR* 3.8 22.4 - - + -
348O VAL* 5.8 2.5 - - + -
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Residues in contact with ASP 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O LEU 4.7 0.2 - - - +
135O GLU* 4.0 10.3 - - - +
136O THR* 2.7 33.6 + - - +
137O GLY 3.1 14.8 + - - +
138O ILE 3.0 24.0 + - - +
139O LYS* 4.0 5.6 - - - +
141O VAL* 1.3 76.5 - - - +
143O LEU* 1.3 56.8 + - + +
146O PRO* 3.6 14.2 - - - +
367O HIS* 3.2 20.1 - - - -
432O VAL 3.3 15.9 - - - +
433O ARG 4.4 0.3 - - - -
434O LEU* 4.0 29.0 + - + +
437O THR* 4.7 6.9 + - - +
438O VAL* 6.1 0.2 - - - -
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Residues in contact with LEU 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139O LYS 3.4 15.5 + - - +
140O VAL 4.2 0.9 - - - +
141O VAL 2.8 1.6 + - - -
142O ASP* 1.3 79.8 - - - +
144O LEU* 1.3 72.5 - - + +
145O ALA 3.5 0.9 - - - -
146O PRO* 4.2 0.8 - - - +
358O LEU* 3.5 12.8 - - - +
367O HIS* 3.1 36.4 + - + +
370O VAL* 4.4 11.2 - - + -
371O ALA* 3.8 11.8 - - + +
374O VAL* 4.4 14.4 - - + -
414O LEU* 5.5 1.3 - - + -
437O THR* 4.6 4.9 - - + -
438O VAL* 4.0 29.4 - - + +
441O PHE* 4.0 42.2 - - + -
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Residues in contact with LEU 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140O VAL* 2.9 31.8 + - + +
143O LEU* 1.3 90.9 - - + +
145O ALA* 1.3 63.4 + - + +
146O PRO* 3.9 2.0 - - - -
350O PRO* 3.4 39.7 - - + +
353O SER* 3.6 12.4 - - - +
354O LYS* 5.0 0.2 - - - -
355O SER* 4.8 2.4 + - - -
358O LEU* 4.1 19.7 - - - +
371O ALA* 4.4 8.7 - - + +
374O VAL* 4.2 20.2 - - + -
375O GLN* 4.1 28.7 + - + +
414O LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140O VAL 3.9 1.0 + - - -
141O VAL* 2.9 23.8 + - - +
144O LEU* 1.3 83.3 - - + +
146O PRO* 1.3 70.9 - - - +
147O TYR* 3.6 7.6 + - - -
331O ALA* 5.1 0.6 - - + +
332O THR 4.1 8.5 - - - +
333O THR* 4.0 20.2 - - + -
353O SER* 3.9 17.5 - - - +
354O LYS 4.2 0.4 - - - +
355O SER* 3.6 16.4 - - - -
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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