Contacts of the helix formed by residues 138 - 145 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136X THR* 3.6 5.5 + - - +
137X GLY* 1.3 85.2 - - - +
139X LYS* 1.3 70.3 + - - +
140X VAL* 4.3 16.6 - - + +
141X VAL* 3.3 16.1 + - + +
142X ASP* 3.0 25.8 + - - +
166X PHE* 4.0 24.0 - - + -
169X GLU* 4.4 10.8 - - + -
170X LEU* 4.9 13.5 - - + +
173X ASN* 4.6 8.5 - - - +
346X PRO* 4.7 2.2 - - + -
416X GLN* 3.7 9.2 - - + +
418X PHE* 3.4 44.9 - - + -
432X VAL 5.1 0.7 - - - -
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Residues in contact with LYS 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLY 4.2 0.6 - - - -
138X ILE* 1.3 70.2 - - - +
140X VAL* 1.3 66.4 + - - +
142X ASP* 4.9 0.4 - - - -
143X LEU* 2.9 28.1 + - - +
413X PHE* 2.8 37.2 + - + +
414X LEU* 4.4 5.6 - - - +
415X SER 3.3 6.5 + - - -
416X GLN* 2.7 36.5 + - - +
432X VAL* 4.2 11.0 - - + +
437X THR* 3.6 32.2 + - + +
440X SER* 6.2 0.2 - - - -
441X PHE* 4.0 18.4 - - + -
460X VAL* 3.0 15.9 + - - +
461X GLY 3.0 30.5 + - - +
462X GLY* 5.3 0.7 - - - -
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Residues in contact with VAL 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X ILE* 3.5 6.9 - - + -
139X LYS* 1.3 75.3 - - + +
141X VAL* 1.3 65.6 + - + +
144X LEU* 3.4 29.9 + - + +
145X ALA* 4.1 0.3 + - - +
346X PRO* 4.1 22.7 - - + +
348X VAL* 3.5 40.4 - - + +
350X PRO* 5.3 3.6 - - + -
353X SER* 6.4 0.2 - - - -
414X LEU* 3.1 54.7 - - + +
416X GLN* 5.4 0.2 - - - +
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Residues in contact with VAL 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X THR* 3.8 14.1 - - + +
138X ILE* 3.3 15.6 + - + +
139X LYS 3.2 0.8 - - - -
140X VAL* 1.3 76.8 - - + +
142X ASP* 1.3 64.7 + - - +
143X LEU 3.2 0.2 + - - -
145X ALA* 2.8 52.9 + - - +
146X PRO* 4.5 0.2 - - + -
147X TYR* 3.3 48.0 - - + +
166X PHE* 3.5 24.5 - - + -
333X THR* 4.2 11.0 - - + -
348X VAL* 5.6 1.1 - - + -
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Residues in contact with ASP 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X LEU 4.1 7.4 - - - +
135X GLU* 4.8 1.1 - - - +
136X THR* 2.7 39.7 + - - +
137X GLY* 3.0 18.0 + - - -
138X ILE 3.0 15.5 + - - +
139X LYS* 4.0 2.9 - - - +
141X VAL* 1.3 80.6 - - - +
143X LEU* 1.3 62.2 + - - +
146X PRO* 3.5 18.5 - - - +
367X HIS* 3.3 19.5 + - - -
432X VAL 4.2 4.3 - - - +
433X ARG 5.0 0.2 - - - -
434X LEU* 4.3 36.4 + - + +
437X THR* 5.1 5.1 + - - +
438X VAL* 6.0 0.2 - - - -
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Residues in contact with LEU 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS 2.9 16.3 + - - +
140X VAL* 4.3 2.5 - - - +
142X ASP* 1.3 77.5 - - - +
144X LEU* 1.3 73.6 + - + +
146X PRO* 5.2 0.2 - - - -
358X LEU* 4.6 0.5 - - - +
367X HIS* 3.0 27.9 + - + +
370X VAL* 4.0 24.0 - - + -
371X ALA* 3.3 18.8 - - + +
374X VAL* 4.5 9.6 - - + -
414X LEU* 4.4 9.6 - - + -
437X THR* 4.1 10.0 - - + +
438X VAL* 4.6 18.6 - - + -
441X PHE* 3.6 43.5 - - + -
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Residues in contact with LEU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X VAL* 3.4 16.2 + - + +
141X VAL 3.3 1.2 + - - -
143X LEU* 1.3 89.8 - - + +
145X ALA* 1.3 61.5 + - + +
146X PRO* 3.3 7.2 - - - +
350X PRO* 3.9 37.0 - - + +
353X SER* 5.0 7.6 - - - +
354X LYS* 5.3 0.5 - - - -
355X SER* 4.8 2.3 + - - -
358X LEU* 3.2 26.8 - - + +
371X ALA* 3.6 38.1 - - + +
374X VAL* 4.3 10.5 - - + -
375X GLN* 3.9 22.7 + - + +
414X LEU* 4.6 15.7 - - + -
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Residues in contact with ALA 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X VAL 4.1 0.8 + - - +
141X VAL* 2.8 34.4 + - - +
144X LEU* 1.3 76.1 - - + +
146X PRO* 1.3 63.3 - - - +
147X TYR* 3.6 6.1 + - - -
331X ALA* 5.2 0.4 - - + -
332X THR 4.3 2.2 - - - +
333X THR* 4.2 11.7 - - + -
353X SER* 4.1 23.8 - - - -
354X LYS 3.8 23.8 - - - +
355X SER* 3.9 6.7 - - - -
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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