Contacts of the strand formed by residues 273 - 280 (chain B) in PDB entry 2Q4E
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 GLU 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ASN* 5.5 0.5 + - - -
268B PRO* 4.2 5.4 - - - +
269B TYR 5.5 0.2 + - - -
270B LYS* 2.6 29.7 + - + +
271B GLU 4.3 0.3 - - - -
272B THR* 1.3 89.7 + - + +
274B ALA* 1.3 64.6 + - - +
275B SER* 5.7 1.1 - - - +
299B THR* 5.0 14.7 - - + +
300B VAL 3.2 18.0 - - - +
301B LYS* 3.0 37.8 + - - -
302B THR* 3.7 5.4 + - - -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASN* 3.9 14.4 - - - +
136B ARG* 3.4 37.7 - - + +
264B ASP* 5.3 2.7 - - - -
268B PRO* 5.1 2.2 - - + -
273B GLU* 1.3 78.1 - - - +
275B SER* 1.3 63.6 + - - +
276B PHE* 4.8 1.2 - - - -
298B HIS 4.7 0.2 - - - -
299B THR* 3.4 0.6 - - - -
300B VAL* 2.8 50.5 + - + +
302B THR* 4.4 1.1 - - + -
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 2.8 28.7 + - - +
262B VAL* 4.0 5.0 - - - +
264B ASP* 3.9 7.6 + - - +
273B GLU* 5.7 1.0 - - - +
274B ALA* 1.3 74.9 + - - +
276B PHE* 1.3 61.0 + - - +
297B GLU* 3.8 17.4 - - - +
298B HIS 3.0 14.6 - - - -
299B THR* 2.9 25.5 - - - +
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Residues in contact with PHE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.9 20.2 - - + -
139B LEU* 4.0 43.7 - - + -
140B LEU* 3.5 29.4 - - + -
143B PHE* 5.4 5.6 - + + -
260B LEU* 4.2 6.1 - - + -
261B ARG 3.5 10.1 - - - +
262B VAL* 4.5 2.7 - - + +
274B ALA 4.8 2.9 - - - -
275B SER* 1.3 77.5 - - - +
277B THR* 1.3 59.0 + - - +
278B THR* 3.9 14.4 - - - -
297B GLU* 3.2 4.7 - - - -
298B HIS* 2.9 66.1 + + + -
299B THR 4.9 1.6 - - - -
300B VAL* 5.3 2.9 - - + -
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B THR 3.8 0.7 - - - +
260B LEU* 3.6 6.1 - - - +
261B ARG* 2.7 58.9 + - + +
276B PHE* 1.3 73.2 - - - +
278B THR* 1.3 67.1 + - - +
295B PRO* 3.3 30.3 - - + -
296B SER 3.0 13.6 + - - +
297B GLU* 2.8 27.4 + - - +
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PHE* 3.3 44.3 - - + -
149B ARG* 5.7 1.1 - - - +
259B THR 3.6 2.9 - - - -
260B LEU* 4.7 0.3 - - - +
276B PHE* 3.9 13.9 - - - -
277B THR* 1.3 77.3 + - - +
279B SER* 1.3 66.4 + - - +
280B THR* 4.1 7.4 - - - +
295B PRO* 3.5 0.7 - - - +
296B SER* 2.6 44.6 + - - -
298B HIS* 3.5 22.4 + - + +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASN* 3.5 6.3 + - - -
247A LEU 4.5 1.9 + - - -
143B PHE* 4.3 0.5 - - - -
258B GLY* 3.1 5.5 - - - -
259B THR* 2.8 50.2 + - - -
261B ARG* 5.8 0.9 - - - -
278B THR* 1.3 78.4 - - - +
280B THR* 1.3 63.0 + - - +
282B ALA* 3.6 23.6 - - - +
291B TRP* 4.4 3.6 - - - -
293B SER 5.3 0.7 + - - -
295B PRO* 4.2 26.1 - - - +
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE* 4.0 7.1 - - - -
148B GLU 4.4 2.0 - - - +
149B ARG* 2.7 50.7 + - + +
257B LYS 3.0 4.7 - - - +
278B THR* 4.1 5.1 - - - +
279B SER* 1.3 73.6 + - - +
281B LYS* 1.3 88.8 + - + +
282B ALA* 3.3 3.3 + - - +
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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