Contacts of the helix formed by residues 277 - 288 (chain B) in PDB entry 4LOE
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 CYS 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B LYS* 3.8 34.5 - - - -
136B GLN* 4.7 0.7 - - - +
275B CYS* 3.5 3.7 - - - +
276B ALA* 1.3 81.8 - - + +
278B PRO* 1.3 66.0 - - - +
279B GLY 3.2 3.3 + - - -
280B ARG* 3.3 50.6 + - - +
281B ASP* 3.0 25.6 + - - -
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Residues in contact with PRO 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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122B VAL* 4.1 6.7 - - + +
123B THR 3.5 24.7 - - - +
125B THR* 4.1 8.5 - - + +
134B PHE* 3.5 27.8 - - + +
135B CYS 3.7 17.5 - - - -
136B GLN* 3.6 15.3 - - + +
275B CYS* 3.7 13.9 - - - +
276B ALA 3.4 7.9 - - - +
277B CYS* 1.3 88.2 - - - +
279B GLY* 1.3 57.9 + - - +
281B ASP* 3.8 0.2 - - - +
282B ARG* 2.8 33.6 + - - +
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Residues in contact with GLY 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.4 42.5 - - - +
119B ALA 4.0 8.3 - - - -
120B LYS 5.3 0.4 + - - -
122B VAL* 4.0 9.5 + - - +
125B THR* 4.3 2.7 - - - -
277B CYS* 3.2 3.5 - - - -
278B PRO* 1.3 79.2 - - - +
280B ARG* 1.3 60.7 + - - +
283B ARG* 3.1 20.3 + - - +
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Residues in contact with ARG 280 (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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118B THR 4.2 1.1 + - - -
120B LYS* 5.2 3.4 - - + +
276B ALA* 5.1 6.1 - - - +
277B CYS* 3.3 46.5 + - - +
279B GLY* 1.3 74.6 - - - +
281B ASP* 1.3 70.9 + - - +
283B ARG* 3.3 6.6 + - - +
284B THR* 2.9 42.6 + - - +
148D ASP* 5.2 7.1 + - - -
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Residues in contact with ASP 281 (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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134B PHE* 3.8 10.1 - - + -
273B ARG* 2.8 38.0 + - - +
275B CYS* 3.2 22.1 - - - +
277B CYS 3.0 18.9 + - - +
278B PRO 3.8 3.1 - - - +
280B ARG* 1.3 96.2 + - - +
282B ARG* 1.3 57.3 + - - +
284B THR* 3.5 5.7 + - - -
285B GLU* 3.0 34.3 + - - +
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Residues in contact with ARG 282 (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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115B HIS* 6.2 0.4 - - - +
116B SER 5.3 1.6 - - - +
117B GLY* 3.9 19.3 + - - +
118B THR* 3.8 15.0 - - + +
125B THR* 2.8 39.4 + - + -
126B TYR 3.1 19.0 + - - -
127B SER* 3.6 13.9 - - - +
128B PRO* 3.7 13.1 - - - +
134B PHE* 3.6 29.9 - - + -
278B PRO 2.8 21.2 + - - +
279B GLY 4.0 2.7 - - - +
281B ASP* 1.3 69.0 - - - +
283B ARG* 1.3 67.2 + - - +
285B GLU* 3.3 1.0 + - - +
286B GLU* 2.7 57.8 + - + +
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Residues in contact with ARG 283 (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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118B THR* 3.0 48.0 + - + +
119B ALA* 4.2 5.5 - - - +
120B LYS 5.3 0.6 - - - +
279B GLY 3.1 14.6 + - - +
280B ARG* 3.8 6.9 - - - +
282B ARG* 1.3 80.6 - - - +
284B THR* 1.3 64.3 + - - +
286B GLU* 4.0 7.1 - - - +
287B GLU* 3.3 21.4 + - - +
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Residues in contact with THR 284 (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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280B ARG* 2.9 28.3 + - - +
281B ASP* 3.7 7.0 - - - +
283B ARG* 1.3 76.1 - - - +
285B GLU* 1.3 67.2 + - + +
287B GLU* 3.1 26.3 + - - +
288B ASN* 3.8 10.9 + - - +
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Residues in contact with GLU 285 (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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130B LEU* 3.7 23.4 - - + +
132B LYS* 3.1 34.5 + - - +
134B PHE* 3.4 20.5 - - + -
273B ARG* 3.4 24.5 + - - +
281B ASP 3.0 21.6 + - - +
282B ARG 3.9 2.7 - - - +
284B THR* 1.3 79.6 - - + +
286B GLU* 1.3 61.4 + - - +
288B ASN* 3.5 25.8 + - - +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 5.0 2.9 - - - +
127B SER* 2.9 24.3 + - - +
128B PRO* 4.6 1.2 - - - +
129B ALA* 5.1 9.1 - - + +
130B LEU* 4.3 10.3 - - + -
282B ARG* 2.7 61.7 + - + +
283B ARG* 4.0 8.4 - - - +
285B GLU* 1.3 73.3 - - - +
287B GLU* 1.3 64.6 + - - +
288B ASN* 3.1 3.6 + - - -
289B LEU* 3.6 14.7 + - - +
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Residues in contact with GLU 287 (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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283B ARG* 3.3 12.4 + - - +
284B THR* 3.1 18.1 + - - +
286B GLU* 1.3 78.2 - - - +
288B ASN* 1.3 61.7 + - - +
289B LEU* 2.9 19.2 + - - +
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Residues in contact with ASN 288 (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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130B LEU* 6.1 0.5 - - - +
284B THR* 3.8 15.2 + - - +
285B GLU* 3.5 17.4 + - - +
286B GLU 3.1 4.1 - - - -
287B GLU* 1.3 77.3 - - - +
289B LEU* 1.3 64.9 + - - +
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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
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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