Contacts of the strand formed by residues 234 - 242 (chain U) in PDB entry 2FD6
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 GLN 234 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200U ASN* 5.8 0.9 - - - +
228U THR* 3.0 21.0 - - - -
229U HIS 3.1 8.7 + - - +
230U GLU* 3.0 53.1 - - + +
231U PRO* 3.3 4.1 - - - +
232U LYS* 2.9 67.3 + - - +
233U ASN* 1.3 74.1 - - - +
235U SER* 1.3 67.0 + - - +
236U TYR* 4.1 0.2 - - - +
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Residues in contact with SER 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199U GLY 3.9 1.9 - - - +
200U ASN* 3.0 30.8 + - - +
226U THR* 5.6 4.7 - - - -
227U GLY 3.3 9.4 - - - -
228U THR* 4.9 0.4 - - - -
230U GLU* 5.1 1.4 - - - +
233U ASN 3.2 6.0 + - - -
234U GLN* 1.3 73.8 - - - +
236U TYR* 1.3 63.6 + - - +
400U NDG 3.9 12.0 + - - +
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Residues in contact with TYR 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198U LYS* 4.0 19.6 - - - +
199U GLY* 3.4 36.6 - - - -
200U ASN* 5.4 0.2 - - - -
225U ALA 4.4 0.2 - - - -
226U THR* 3.3 9.2 - - - +
227U GLY 2.8 27.8 + - - +
229U HIS* 3.3 53.6 + + + +
230U GLU* 5.1 8.5 - - + +
234U GLN 3.2 0.2 + - - -
235U SER* 1.3 76.7 - - - +
237U MET* 1.3 69.6 + - - +
238U VAL* 3.8 16.1 - - + +
256U PHE 4.0 10.8 - - - -
258U MET* 3.4 31.9 - - + -
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Residues in contact with MET 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198U LYS* 3.3 2.1 - - - -
199U GLY 2.9 35.5 + - - +
200U ASN* 4.8 1.8 - - - -
201U SER* 3.8 26.5 - - - +
205U CYS* 3.3 35.4 - - - -
224U VAL* 4.5 4.7 - - + -
225U ALA 3.0 12.6 - - - +
226U THR* 3.9 18.4 - - + +
236U TYR* 1.3 80.3 - - - +
238U VAL* 1.3 76.1 + - - +
239U ARG* 3.6 31.6 - - - +
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Residues in contact with VAL 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159U PHE* 3.8 17.5 - - + -
161U ASN* 3.5 24.9 - - - +
197U CYS 3.6 7.0 - - - +
198U LYS* 4.9 4.3 - - + -
223U LEU* 4.0 2.7 - - - +
224U VAL* 3.4 3.8 - - - +
225U ALA* 2.8 31.9 + - + +
236U TYR* 3.8 20.2 - - + +
237U MET* 1.3 83.1 - - - +
239U ARG* 1.3 67.2 + - - +
256U PHE* 4.3 16.8 - - + +
258U MET* 3.7 20.9 - - + -
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Residues in contact with ARG 239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159U PHE* 4.0 4.7 - - - -
161U ASN* 3.3 22.0 + - - +
195U TYR* 3.3 15.5 - - - +
196U SER* 3.4 8.5 - - - -
197U CYS* 3.2 34.5 + - - +
201U SER* 5.9 0.6 - - - -
205U CYS* 4.5 0.8 + - - -
210U THR* 4.5 8.1 - - - -
223U LEU* 3.2 13.7 - - - +
224U VAL* 3.3 26.6 - - + +
237U MET* 3.6 30.6 - - + +
238U VAL* 1.3 80.5 - - - +
240U GLY* 1.3 59.4 + - - +
272U ASN* 2.7 37.7 + - - +
273U HIS 3.6 10.7 + - - -
274U PRO* 3.7 29.9 - - - +
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Residues in contact with GLY 240 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159U PHE* 3.7 13.8 - - - -
160U HIS 3.7 7.2 - - - -
161U ASN* 3.9 3.4 - - - -
194U CYS* 3.7 3.9 - - - +
195U TYR 3.2 12.2 + - - -
213U ILE* 4.3 5.4 - - - -
222U CYS* 3.6 3.1 - - - -
223U LEU 2.8 29.0 + - - -
239U ARG* 1.3 75.2 - - - +
241U CYS* 1.3 63.7 + - - -
272U ASN* 3.5 4.5 - - - +
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Residues in contact with CYS 241 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159U PHE* 3.1 6.6 - - - -
160U HIS* 3.0 50.8 + - + -
194U CYS* 3.9 6.3 - - - -
213U ILE* 3.9 21.1 - - - -
215U CYS* 2.0 60.1 - - + -
219U MET* 3.9 4.7 - - - +
221U GLN 3.3 4.5 - - - -
240U GLY* 1.3 73.2 - - - -
242U ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158U GLY 3.3 12.1 - - - +
159U PHE* 4.0 4.5 - - + -
219U MET* 3.6 8.2 - - - +
220U ASN 3.1 6.4 + - - -
221U GLN* 2.7 39.8 + - + +
223U LEU* 3.7 35.0 - - + -
241U CYS* 1.3 76.3 - - - +
243U THR* 1.3 68.0 + - - +
246U MET* 3.9 4.7 - - + -
247U CYS* 5.2 0.2 - - - -
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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