Contacts of the strand formed by residues 237 - 246 (chain A) in PDB entry 4FLL
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 TYR 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLU* 4.0 12.4 + - + +
144A ASP* 2.6 51.2 + - + -
147A GLY* 3.8 25.1 - - - +
148A MET* 3.8 27.8 - - + -
151A VAL* 3.4 13.0 - - + +
233A TYR* 3.2 6.8 - - - -
234A ARG 2.8 33.6 + - - +
235A ASN* 3.2 29.8 - - + -
236A GLY* 1.3 82.6 - - - +
238A HIS* 1.4 60.2 + - - +
306A HIS* 3.3 9.0 - - + -
307A LYS* 3.8 31.4 + - + -
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Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PRO* 4.2 2.2 - - + +
117A TYR* 3.3 28.8 + + - -
148A MET* 3.1 26.7 - - - +
151A VAL* 3.6 3.6 - - - -
191A SER* 2.8 32.7 + - - -
231A THR* 4.3 2.0 - - + -
232A LEU 3.1 4.9 - - - -
233A TYR* 3.3 31.9 - + - -
237A TYR* 1.4 74.9 - - - +
239A GLY* 1.3 59.2 + - - +
305A ILE* 3.6 26.5 - - + +
306A HIS 2.8 14.3 + - - +
307A LYS 3.8 7.4 + - - -
308A LEU 3.7 1.0 - - - -
309A PHE* 3.5 33.6 + + + +
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.6 9.4 - - - +
152A CYS* 3.6 24.7 - - - -
155A ALA* 3.7 12.9 - - - +
231A THR* 3.1 5.2 - - - -
232A LEU 2.9 32.3 + - - -
238A HIS* 1.3 74.5 - - - +
240A ASP* 1.3 61.0 + - - -
305A ILE* 4.2 0.7 - - - -
369A THR* 4.6 0.4 - - - -
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 3.1 2.6 - - - +
230A ILE 3.5 1.8 - - - -
231A THR* 2.8 19.9 + - - +
239A GLY* 1.3 74.2 - - - +
241A LEU* 1.4 67.4 + - - +
303A HIS* 3.0 9.9 + - - -
305A ILE* 3.4 17.9 - - + +
309A PHE* 3.7 5.1 - - - -
334A THR* 4.2 1.3 - - + -
367A GLU* 2.9 10.6 - - - +
368A HIS 3.9 2.1 - - - -
369A THR* 2.7 37.4 + - - +
381A THR* 3.6 3.0 - - - +
501A MN 2.1 28.8 + - - -
502A MN 2.0 33.3 + - - -
503A YZ6 3.3 1.9 + - - -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA* 3.5 42.4 - - + +
156A ARG* 3.6 47.3 - - - +
159A LEU* 3.7 17.5 - - + -
229A ASP* 3.1 3.8 - - - +
230A ILE* 2.9 43.0 + - + +
240A ASP* 1.4 78.2 + - - +
242A ASN* 1.4 62.7 + - - +
367A GLU* 3.5 21.1 - - - +
368A HIS* 5.0 0.2 - - - +
381A THR* 3.7 19.3 - - + +
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Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 5.8 0.2 + - - -
159A LEU* 4.4 2.5 - - - -
227A ASN* 2.9 30.1 + - - +
228A VAL 3.2 16.2 - - - +
229A ASP* 2.8 26.2 + - - -
241A LEU* 1.4 78.4 - - - +
243A GLU* 1.3 71.9 - - - +
365A GLN* 3.2 22.2 + - - +
366A PHE* 3.1 20.6 - - - -
367A GLU* 3.1 47.8 + - - +
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 2.9 35.6 + - - +
159A LEU* 3.7 10.7 - - + +
227A ASN* 3.2 8.1 + - - -
228A VAL 3.1 27.7 + - - -
242A ASN* 1.3 81.6 - - - +
244A THR* 1.4 60.0 + - - +
245A PHE* 3.6 19.6 - - + -
366A PHE* 3.7 17.8 - - + -
383A ARG* 4.6 0.7 - - - -
389A PRO* 3.8 16.8 - - - +
390A HIS* 3.0 46.8 + - - +
391A PHE 4.6 0.5 + - - -
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Residues in contact with THR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 4.0 20.0 - - + -
226A VAL 3.4 13.2 - - - +
227A ASN* 3.2 8.5 + - + +
243A GLU* 1.4 74.1 - - - +
245A PHE* 1.3 68.2 + - - +
258A VAL* 3.8 26.6 - - + +
363A SER 5.6 0.2 - - - +
364A ALA* 4.1 8.0 - - + -
365A GLN 2.7 37.2 + - - -
366A PHE* 3.5 27.8 - - - -
391A PHE* 3.8 13.9 + - - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 3.9 15.7 - - + -
163A ALA* 3.5 36.6 - - + -
166A ILE* 4.0 31.0 - - + -
225A ILE* 3.4 7.8 - - - +
226A VAL* 2.7 45.7 + - - +
228A VAL* 3.8 26.7 - - + -
243A GLU* 3.6 33.9 - - + -
244A THR* 1.3 77.8 - - - +
246A PHE* 1.4 66.0 + - - +
390A HIS* 3.5 25.6 - + + -
391A PHE* 4.7 6.1 - - - +
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.6 15.3 - - - +
224A ASP 3.8 3.4 - - - -
225A ILE* 4.1 6.7 - - + -
245A PHE* 1.4 78.4 - - - +
247A VAL* 1.3 62.4 + - - +
248A GLY 3.6 12.9 + - - +
250A VAL* 3.5 35.4 - - + -
254A ALA 4.0 6.5 - - - -
255A ARG* 4.0 29.6 - - + -
258A VAL* 3.8 29.2 - - + -
391A PHE* 3.6 50.7 - + + +
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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