Contacts of the strand formed by residues 198 - 204 (chain L) in PDB entry 1FSK
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 VAL 198 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143L LEU* 3.9 24.5 - - + -
159L TRP* 3.6 29.8 - - + -
160L ASN* 3.4 13.2 - - - +
164L LEU* 4.3 15.7 - - + -
186L VAL* 5.0 2.2 - - + -
188L VAL* 5.2 10.1 - - + -
192L THR 5.8 0.9 - - - +
193L TRP* 4.1 22.0 - - + +
196L GLU* 4.1 2.1 + - + -
197L THR* 1.3 81.1 + - - +
199L THR* 1.3 68.6 + - - +
214L LYS* 3.6 5.9 - - - +
215L ILE* 3.0 26.4 + - + +
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Residues in contact with THR 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L TRP* 3.4 5.5 - - - -
160L ASN* 2.6 57.4 + - - +
197L THR* 4.6 7.6 - - - +
198L VAL* 1.3 82.4 - - - +
200L CYS* 1.3 63.1 + - - +
201L ASN* 3.7 6.6 + - - +
212L ASP* 4.2 6.8 - - - +
213L LYS 2.9 24.1 + - - -
214L LYS* 3.7 10.2 + - - +
215L ILE 4.3 1.1 - - - +
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Residues in contact with CYS 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L VAL* 4.4 6.3 - - - -
145L CYS* 2.6 43.7 - - - -
157L VAL* 5.8 5.2 - - + -
158L THR 3.3 6.3 - - - +
159L TRP* 3.5 27.1 - - + -
199L THR* 1.3 72.8 + - - +
201L ASN* 1.3 61.1 + - - +
202L VAL* 5.2 4.3 - - + -
211L VAL 3.7 1.2 - - - +
212L ASP* 3.3 4.7 - - - -
213L LYS* 3.0 42.9 + - - -
215L ILE* 5.1 0.7 - - - -
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Residues in contact with ASN 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L THR* 3.8 1.2 + - - +
157L VAL* 3.3 3.9 - - - -
158L THR* 2.5 67.0 + - - +
160L ASN* 3.5 2.1 + - - +
161L SER* 2.5 44.7 + - - +
199L THR* 3.7 12.0 + - - +
200L CYS* 1.3 74.2 - - - +
202L VAL* 1.3 62.2 + - - +
203L ALA* 4.0 0.9 + - - +
210L LYS* 5.9 6.1 - - + -
212L ASP* 3.2 23.5 - - - +
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Residues in contact with VAL 202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L PRO* 4.9 7.2 - - + -
126L VAL* 3.6 36.1 - - + -
147L VAL* 3.6 31.9 - - + -
155L VAL* 4.2 12.3 - - + -
156L THR 3.5 8.1 - - - +
157L VAL* 4.1 11.4 - - + +
200L CYS* 3.8 6.0 - - - +
201L ASN* 1.3 74.0 - - - +
203L ALA* 1.3 62.1 + - - +
204L HIS 4.5 0.2 + - - -
210L LYS* 3.5 4.0 - - - +
211L VAL* 2.8 54.6 + - + +
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Residues in contact with ALA 203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L VAL* 3.3 6.5 - - - +
156L THR* 2.6 54.9 + - + +
201L ASN 4.0 1.3 + - - +
202L VAL* 1.3 75.1 - - - +
204L HIS* 1.3 61.1 + - - +
205L PRO* 3.8 6.6 - - + +
209L THR 3.8 4.0 - - - +
210L LYS* 3.6 33.0 - - + -
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Residues in contact with HIS 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L THR 3.8 8.7 - - - -
124L PRO* 3.9 19.0 - - + +
150L TYR* 3.6 10.8 - + - -
151L PHE 3.4 18.8 - - - -
152L PRO 2.9 23.1 + - - -
154L PRO 3.4 19.5 - - - -
155L VAL* 3.5 18.2 - - + -
203L ALA* 1.3 71.7 - - - +
205L PRO* 1.3 70.8 - - - +
206L ALA* 3.4 19.9 - - + +
207L SER* 2.6 44.4 + - - +
209L THR 3.0 26.5 + - - +
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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