Contacts of the strand formed by residues 215 - 220 (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 VAL 215 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92X LEU* 3.8 4.6 - - - +
93X GLY* 2.8 24.4 + - - -
182X SER* 3.1 26.5 - - - +
183X VAL 4.7 0.2 - - - -
184X PHE* 4.3 9.2 - - + +
201X MET* 4.8 7.6 - - + -
206X VAL* 3.7 22.2 - - + +
207X ILE* 3.5 32.5 - - + +
213X SER* 4.3 0.5 + - - -
214X LYS* 1.3 79.8 - - - +
216X ALA* 1.3 73.0 + - - +
217X LEU* 4.2 12.6 + - + +
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Residues in contact with ALA 216 (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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91X THR* 3.5 39.9 - - - +
92X LEU* 3.9 8.5 - - + +
93X GLY 4.1 0.4 - - - +
94X ARG 4.7 0.4 - - - +
96X ILE* 6.3 1.1 - - + -
182X SER 3.1 8.8 + - - +
183X VAL* 3.7 5.7 - - + +
184X PHE 3.2 24.4 + - - +
215X VAL* 1.3 75.6 - - - +
217X LEU* 1.3 63.7 + - - +
218X VAL* 5.2 2.5 - - + -
239X ILE* 4.5 16.2 - - + -
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Residues in contact with LEU 217 (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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93X GLY 6.0 0.7 - - - -
94X ARG 3.1 23.2 + - - +
95X ILE* 3.7 26.0 - - + -
96X ILE* 3.2 15.2 + - - +
184X PHE* 3.9 25.8 - - + -
197X LEU* 5.4 6.1 - - + -
198X TYR* 3.5 37.9 - - + +
201X MET* 5.6 4.3 - - + -
207X ILE* 3.8 20.0 - - + -
215X VAL* 4.2 12.3 - - + +
216X ALA* 1.3 74.3 - - - +
218X VAL* 1.3 68.5 + - - +
219X PHE* 3.8 20.0 - - + -
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Residues in contact with VAL 218 (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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96X ILE* 3.7 28.0 - - + +
97X ASN 4.7 0.4 - - - +
183X VAL* 5.1 2.0 - - + -
184X PHE 3.1 13.8 + - - +
185X THR* 3.5 4.0 - - + +
186X GLY 2.8 26.3 + - - +
216X ALA* 4.9 4.0 - - + +
217X LEU* 1.3 82.1 - - - +
219X PHE* 1.3 66.7 + - - +
232X VAL* 3.5 26.2 - - + +
235X THR* 4.1 9.6 - - + -
236X GLY* 3.7 35.9 - - - +
239X ILE* 4.6 6.3 - - + -
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Residues in contact with PHE 219 (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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138T ILE* 4.0 21.8 - - + -
95X ILE* 3.6 24.2 - - + -
96X ILE 3.4 14.7 + - - +
97X ASN* 4.0 10.4 - - - +
98X VAL 4.8 1.0 + - - -
103X ILE* 4.4 4.8 - - + +
184X PHE* 3.9 22.2 - + - -
186X GLY* 3.8 16.8 - - - -
194X GLY* 3.7 29.4 - - - -
197X LEU* 4.7 4.9 - - + -
217X LEU* 3.8 30.3 - - + -
218X VAL* 1.3 79.8 - - - +
220X GLY* 1.3 58.5 + - - +
221X GLN* 3.4 35.2 - - + -
224X GLU* 3.9 8.1 - - - +
232X VAL* 4.0 7.9 - - - +
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Residues in contact with GLY 220 (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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98X VAL* 6.1 1.1 - - - -
186X GLY 3.1 12.6 + - - +
187X VAL* 4.0 1.4 - - - -
188X GLY* 2.9 18.9 + - - -
219X PHE* 1.3 73.6 - - - +
221X GLN* 1.3 64.8 + - - +
224X GLU* 3.6 19.1 - - - -
228X ALA* 5.4 2.2 - - - -
229X ARG* 3.7 9.7 - - - +
232X VAL* 3.9 18.0 - - - +
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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