Contacts of the strand formed by residues 303 - 309 (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 SER 303 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149W ARG* 3.6 27.2 + - - +
150W GLY* 4.6 3.8 - - - -
244W ARG* 3.3 10.2 - - - +
249W GLN 3.0 6.8 + - - +
250W ASP* 2.8 32.6 + - - +
251W VAL* 2.8 28.5 + - - +
297W THR 4.2 4.5 - - - -
298W THR* 4.1 11.0 - - - -
302W GLY* 1.3 76.2 - - - -
304W VAL* 1.3 63.6 + - - +
305W THR* 4.2 2.0 + - - -
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Residues in contact with VAL 304 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150W GLY* 3.5 13.0 - - - -
237W LEU* 4.7 8.1 - - + -
240W ALA* 3.9 25.6 - - + +
241W GLU* 4.6 2.7 - - + -
244W ARG* 3.5 45.3 - - + +
251W VAL* 3.6 9.4 - - + +
253W LEU* 4.4 19.1 - - + -
295W ARG 5.0 0.2 - - - +
296W ILE* 3.1 36.5 - - + +
297W THR 3.6 6.9 + - - -
303W SER* 1.3 75.4 - - - +
305W THR* 1.3 62.7 + - - +
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Residues in contact with THR 305 (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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134W LEU* 3.8 26.5 - - + +
147W TYR* 5.0 3.1 - - + -
148W ALA 3.6 7.4 + - - +
149W ARG* 3.7 1.6 - - - +
150W GLY 2.7 25.8 + - - -
151W GLY 3.6 7.9 - - - +
153W ILE* 3.6 28.9 - - + -
250W ASP* 6.1 0.6 - - - +
251W VAL 2.8 15.8 + - - +
252W LEU* 3.4 12.6 - - + +
253W LEU 2.9 22.1 + - - -
303W SER* 4.2 2.3 + - - -
304W VAL* 1.3 72.2 + - - +
306W SER* 1.3 66.3 + - - +
307W VAL* 5.3 0.2 - - + -
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Residues in contact with SER 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151W GLY 3.1 9.5 + - - -
152W LYS* 3.6 0.2 - - - -
153W ILE* 2.8 36.0 + - - +
253W LEU* 3.1 26.8 - - - +
255W ILE* 5.2 0.7 - - - -
296W ILE* 3.0 31.6 - - - +
305W THR* 1.3 73.0 - - - +
307W VAL* 1.3 58.1 + - - +
308W GLN* 3.4 28.3 - - - -
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Residues in contact with VAL 307 (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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147W TYR* 4.0 27.6 - - + +
153W ILE* 3.6 13.2 - - + +
155W LEU* 4.2 30.7 - - + -
166W PHE* 6.0 0.2 - - + -
167W ILE* 5.3 0.9 - - + -
170W LEU* 4.1 10.3 - - + -
252W LEU* 4.4 13.9 - - + -
253W LEU 2.9 9.2 + - - -
254W PHE* 3.5 38.2 - - + +
255W ILE 3.4 16.8 + - - +
305W THR* 5.3 0.2 - - + -
306W SER* 1.3 75.5 - - - +
308W GLN* 1.3 59.6 + - - +
309W ALA 3.8 0.9 + - - -
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Residues in contact with GLN 308 (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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152W LYS* 3.8 12.8 - - - +
153W ILE 2.8 10.4 + - - +
154W GLY* 3.3 8.7 - - - -
155W LEU* 3.1 17.7 + - - -
255W ILE* 3.4 25.0 - - + +
258W ILE* 3.5 27.4 - - + +
292W LEU* 6.2 0.4 - - - +
293W GLN* 2.8 45.9 + - - +
296W ILE* 3.7 4.4 - - - +
306W SER* 3.4 24.4 - - - -
307W VAL* 1.3 73.0 - - - +
309W ALA* 1.3 64.7 + - - +
310W VAL* 3.5 4.3 - - + +
325W THR* 4.5 3.6 - - - +
329W LEU* 4.3 10.4 - - + +
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Residues in contact with ALA 309 (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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155W LEU* 3.2 28.9 - - + +
157W GLY 6.0 1.3 - - - +
163W LYS* 5.6 9.0 - - + +
255W ILE 3.1 10.6 + - - +
256W ASP* 3.9 25.6 - - + +
257W ASN* 4.1 6.7 - - - +
258W ILE* 3.2 27.0 + - - +
307W VAL 3.8 2.2 + - - -
308W GLN* 1.3 76.3 - - - +
310W VAL* 1.3 58.9 + - - +
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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
------------------------------------------------------------
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