Contacts of the helix formed by residues 188 - 194 (chain K) 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 GLN 188 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K VAL* 4.6 3.2 - - - +
149K GLN 3.0 33.3 + - - +
163K ARG* 4.5 3.6 + - - -
184K THR* 3.3 18.3 + - - +
185K ILE* 3.0 16.2 + - - +
187K ASN* 1.3 74.0 - - - +
189K LYS* 1.3 63.7 + - - +
190K ARG 3.0 4.8 + - - -
191K TRP* 3.2 22.9 + - - +
192K ASN* 3.1 40.9 + - - +
201K LEU* 3.3 46.4 + - + +
203K CYS* 4.3 5.6 - - - -
230K TYR* 3.9 2.7 - - + -
267K LEU* 5.2 0.7 - - + -
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Residues in contact with LYS 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K LEU 3.2 17.0 + - - +
187K ASN 3.0 1.1 - - - -
188K GLN* 1.3 78.5 - - - +
190K ARG* 1.3 63.5 + - + +
192K ASN 4.9 0.2 - - - +
193K ASN* 3.2 42.8 + - - +
225K HIS* 3.3 34.4 + - + +
226K ASP* 4.2 15.3 - - + +
227K ALA* 5.7 0.4 - - + -
230K TYR* 3.5 16.3 + - + +
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Residues in contact with ARG 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K ASN* 2.8 36.1 + - - +
188K GLN 3.0 0.4 - - - -
189K LYS* 1.3 83.2 - - + +
191K TRP* 1.3 88.7 + - + +
193K ASN* 3.8 10.0 + - - +
194K GLY* 4.2 3.8 + - - -
437K PRO* 4.3 6.0 + - - +
438K LEU* 2.9 35.3 + - - +
439K ALA* 3.4 20.7 - - - +
442K GLU* 3.9 8.3 + - - -
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Residues in contact with TRP 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K GLN* 3.0 52.6 - - + +
163K ARG* 5.2 4.9 - - - +
187K ASN* 3.3 40.2 - - - -
188K GLN* 3.2 23.9 + - - +
190K ARG* 1.3 98.4 - - + +
192K ASN* 1.3 66.2 + - - +
193K ASN 3.2 6.5 + - - -
194K GLY* 3.3 11.5 + - - -
196K ASP 4.8 1.7 + - - +
199K LYS* 3.5 51.2 - - + +
200K LYS* 3.4 14.6 - - - +
439K ALA* 6.2 1.1 - - - -
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Residues in contact with ASN 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K GLN* 3.1 19.9 + - - +
189K LYS 4.7 1.1 - - - +
191K TRP* 1.3 78.1 - - - +
193K ASN* 1.3 61.7 + - - +
194K GLY 3.5 0.2 - - - -
200K LYS* 3.6 25.5 + - + +
201K LEU 3.0 40.3 + - - -
202K TYR* 5.1 2.9 - - - -
229K LYS* 5.0 4.3 - - - -
230K TYR* 2.9 61.9 - - + +
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Residues in contact with ASN 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LYS* 3.2 33.2 + - - +
190K ARG 3.8 4.9 + - - +
191K TRP 3.2 0.8 - - - -
192K ASN* 1.3 77.6 - - - +
194K GLY* 1.3 68.2 + - - +
226K ASP* 4.8 3.8 + - - -
229K LYS* 2.9 38.2 + - - +
230K TYR* 5.4 0.3 - - - -
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Residues in contact with GLY 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K ARG 4.2 3.9 + - - -
191K TRP 3.3 11.9 + - - -
193K ASN* 1.3 86.0 - - - +
195K SER* 1.3 64.8 + - - -
196K ASP 3.7 0.9 - - - -
200K LYS* 3.3 19.4 + - - -
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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