Contacts of the strand formed by residues 304 - 309 (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 304 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X GLY* 3.4 8.6 - - - -
151X GLY* 3.6 2.8 + - - +
152X LYS* 6.1 0.2 - - - +
240X ALA* 4.6 5.6 - - + +
244X ARG* 3.9 36.1 - - + -
251X VAL* 3.6 31.6 - - + +
253X LEU* 4.6 13.2 - - + -
296X ILE* 5.3 6.7 - - + -
297X THR* 4.0 14.2 - - - +
298X THR* 2.8 24.1 + - - -
302X GLY 3.7 0.8 + - - +
303X SER* 1.3 78.7 - - - +
305X THR* 1.3 72.3 + - - +
306X SER* 3.8 8.1 + - - +
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Residues in contact with THR 305 (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* 4.0 17.9 - - + -
148X ALA 3.3 23.8 - - - +
149X ARG* 3.7 4.0 - - - +
150X GLY 2.7 19.1 + - - -
151X GLY 3.7 7.0 - - - +
153X ILE* 4.1 10.3 - - + -
174X ILE* 6.2 0.2 - - + -
178X HIS* 5.0 7.6 - - - -
251X VAL 2.9 11.7 + - - -
252X LEU* 3.3 21.5 - - + +
253X LEU 3.0 22.3 + - - -
303X SER* 5.2 1.0 + - - -
304X VAL* 1.3 70.4 - - - +
306X SER* 1.3 61.9 + - - +
307X VAL* 5.4 0.2 - - + -
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Residues in contact with SER 306 (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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151X GLY 3.0 5.8 + - - -
152X LYS* 3.4 27.9 - - - +
153X ILE* 2.7 37.9 + - - +
253X LEU* 3.3 14.8 - - - +
255X ILE* 5.4 0.4 - - - -
296X ILE* 3.7 26.5 - - - +
304X VAL* 3.8 4.8 + - - -
305X THR* 1.3 73.0 - - - +
307X VAL* 1.3 62.0 + - - +
308X GLN* 4.5 10.0 + - - -
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Residues in contact with VAL 307 (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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153X ILE* 3.4 34.8 - - + -
155X LEU* 4.0 16.4 - - + -
167X ILE* 5.4 2.6 - - + +
170X LEU* 3.7 31.9 - - + -
252X LEU* 4.7 6.1 - - + -
253X LEU 2.8 9.2 + - - +
254X PHE* 3.3 36.1 - - + -
255X ILE 3.0 22.9 + - - +
305X THR* 5.4 0.2 - - + -
306X SER* 1.3 76.3 - - - +
308X GLN* 1.3 62.7 + - - +
309X ALA 4.1 0.3 + - - -
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Residues in contact with GLN 308 (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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152X LYS* 4.4 9.5 - - - +
153X ILE 2.8 18.0 + - - +
154X GLY* 3.4 4.2 - - - -
155X LEU* 3.0 30.2 + - - +
255X ILE* 3.5 29.7 - - + +
258X ILE* 3.3 23.8 - - + +
293X GLN* 2.9 47.8 + - - +
296X ILE* 4.2 5.7 - - - +
306X SER* 4.5 10.8 + - - +
307X VAL* 1.3 77.6 - - - +
309X ALA* 1.3 58.2 + - - +
310X VAL* 3.7 6.4 + - + +
329X LEU* 4.3 15.1 - - + +
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Residues in contact with ALA 309 (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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155X LEU* 3.6 13.0 - - + +
163X LYS* 5.1 3.4 - - + -
167X ILE* 3.4 24.2 - - + -
255X ILE 2.6 14.6 + - - +
256X ASP* 3.3 25.4 - - - +
257X ASN* 2.7 20.4 + - - +
258X ILE* 2.9 21.8 + - - +
307X VAL 4.1 0.6 + - - -
308X GLN* 1.3 71.6 - - - +
310X VAL* 1.3 57.4 + - - +
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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