Contacts of the helix formed by residues 138 - 145 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136W THR* 3.3 15.8 + - - +
137W GLY* 1.3 82.2 - - - +
139W LYS* 1.3 69.6 + - - +
140W VAL* 4.3 6.7 - - + +
141W VAL* 3.3 12.9 + - + -
142W ASP* 3.0 26.7 + - - -
166W PHE* 4.2 21.3 - - + -
169W GLU* 4.5 7.9 - - + -
170W LEU* 3.8 28.7 - - + -
173W ASN* 4.2 7.2 - - - +
346W PRO* 4.1 18.2 - - + -
416W GLN* 3.4 8.5 - - + +
418W PHE* 4.0 27.1 - - + -
432W VAL 4.7 0.9 - - - -
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Residues in contact with LYS 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137W GLY 4.1 0.4 + - - -
138W ILE* 1.3 72.4 - - - +
140W VAL* 1.3 63.9 - - - +
141W VAL 3.2 0.7 + - - -
143W LEU* 3.3 28.1 + - - +
413W PHE* 2.7 42.1 + - + +
414W LEU* 4.0 8.3 - - - +
415W SER 2.8 15.9 + - - -
416W GLN* 2.8 26.9 + - - +
432W VAL* 3.9 21.3 - - + -
437W THR* 4.1 16.7 - - + +
441W PHE* 4.6 6.7 - - + -
460W VAL* 2.7 33.1 + - - +
461W GLY 3.1 21.7 + - - +
462W GLY* 5.3 0.2 - - - -
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Residues in contact with VAL 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138W ILE* 3.4 2.1 - - + +
139W LYS* 1.3 75.2 - - - +
141W VAL* 1.3 62.2 + - + +
144W LEU* 3.3 36.9 + - + +
145W ALA* 4.0 1.2 + - - +
344W ILE* 6.3 0.9 - - + -
346W PRO* 4.2 22.2 - - + +
348W VAL* 3.6 43.5 - - + +
350W PRO* 5.0 5.8 - - + -
353W SER* 6.2 0.2 - - - -
414W LEU* 3.0 48.7 - - + +
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Residues in contact with VAL 141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136W THR* 3.9 18.8 - - + +
138W ILE* 3.3 17.6 + - + +
139W LYS 3.2 0.8 - - - -
140W VAL* 1.3 77.5 - - + +
142W ASP* 1.3 70.5 + - - +
143W LEU 3.0 1.6 - - - -
145W ALA* 2.8 50.8 + - - +
147W TYR* 3.3 31.0 - - + +
166W PHE* 3.9 28.7 - - + -
170W LEU* 6.1 0.2 - - + -
333W THR* 4.7 7.9 - - + +
348W VAL* 4.9 3.4 - - + -
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Residues in contact with ASP 142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133W ILE* 5.8 2.8 - - + +
134W LEU 4.1 1.7 - - - +
135W GLU* 4.0 7.6 - - - -
136W THR* 2.7 38.0 + - - +
137W GLY* 3.0 23.0 + - - -
138W ILE 3.0 14.0 + - - +
139W LYS 4.6 0.9 - - - +
141W VAL* 1.3 79.5 - - - +
143W LEU* 1.3 58.0 + - + +
146W PRO* 3.8 19.6 - - - +
367W HIS* 3.2 19.2 + - - -
432W VAL 3.8 6.8 - - - +
434W LEU* 3.5 31.9 + - + +
437W THR* 5.1 4.5 - - - +
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Residues in contact with LEU 143 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139W LYS 3.3 14.8 + - - +
141W VAL 2.9 1.6 + - - -
142W ASP* 1.3 80.7 - - - +
144W LEU* 1.3 80.2 + - + +
145W ALA 3.5 0.4 + - - -
146W PRO* 4.3 0.2 - - - +
358W LEU* 4.3 3.5 - - - +
367W HIS* 3.1 32.1 - - + +
370W VAL* 4.5 10.8 - - + -
371W ALA* 3.7 29.5 - - + +
374W VAL* 4.3 4.9 - - + -
414W LEU* 4.8 1.6 - - + -
434W LEU* 5.1 0.2 - - - -
437W THR* 3.9 15.0 - - + -
438W VAL* 4.9 9.6 - - + -
441W PHE* 3.6 48.2 - - + -
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Residues in contact with LEU 144 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140W VAL* 3.3 18.3 + - + +
143W LEU* 1.3 96.1 - - + +
145W ALA* 1.3 63.3 + - + +
146W PRO* 3.9 1.8 - - - -
350W PRO* 3.7 44.2 - - + +
353W SER* 4.1 6.7 - - - +
354W LYS* 4.6 1.2 - - - -
358W LEU* 3.9 20.2 - - - +
371W ALA* 4.2 7.9 - - + +
374W VAL* 3.7 31.4 - - + -
375W GLN* 4.0 24.4 + - + +
378W LEU* 5.1 0.4 - - + -
414W LEU* 4.1 20.2 - - + -
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Residues in contact with ALA 145 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140W VAL 4.0 0.6 + - - +
141W VAL* 2.8 28.3 + - + +
144W LEU* 1.3 83.6 - - + +
146W PRO* 1.3 69.8 - - - +
147W TYR* 3.5 6.1 + - - -
331W ALA* 5.1 1.8 - - + +
332W THR 4.2 7.2 - - - +
333W THR* 5.7 1.3 - - - +
353W SER* 4.2 10.8 - - - +
354W LYS 3.3 31.6 - - - +
355W SER* 3.6 6.5 - - - -
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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