Contacts of the helix formed by residues 282 - 296 (chain B) in PDB entry 3E61
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 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B THR* 5.7 0.4 - - - -
280B ASP* 3.1 16.8 + - - -
281B GLN* 1.3 78.4 - - - +
283B ALA* 1.3 52.9 + - - +
284B TYR 3.4 2.7 - - - -
285B HIS* 3.3 18.4 + - - +
286B LEU* 2.8 31.9 + - - +
310B ALA* 3.0 32.6 + - - +
312B THR* 6.1 0.2 - - - +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 3.8 43.5 - - + +
76B LEU* 4.1 17.5 - - + -
77B ILE* 3.3 17.4 - - + +
264B ASP 5.2 6.1 - - - +
280B ASP* 5.0 0.8 + - - -
281B GLN* 3.4 4.1 + - + +
282B SER* 1.3 71.7 - - - +
284B TYR* 1.3 65.9 + - - +
286B LEU* 3.3 7.3 - - - +
287B GLY 3.1 16.6 + - - -
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.7 34.6 - - + +
79B ARG* 3.9 5.2 - - + -
80B GLY* 3.3 35.6 - - - -
83B ASP* 2.5 40.2 + - + +
282B SER 3.4 0.6 - - - -
283B ALA* 1.3 76.3 - - - +
285B HIS* 1.3 59.9 + - + +
287B GLY 3.1 14.0 + - - -
288B GLU* 3.1 41.7 + - + -
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Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER* 3.3 20.2 + - - +
284B TYR* 1.3 79.2 - - + +
286B LEU* 1.3 57.6 + - - +
288B GLU* 2.7 33.6 + - - +
289B ILE* 2.8 65.6 + - + +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.3 13.2 - - + -
77B ILE* 3.9 25.8 - - + -
143B ILE* 3.5 30.3 - - + +
153B ILE* 3.5 40.5 - - + +
154B SER* 4.3 6.7 - - - +
155B THR* 5.7 2.5 - - + +
281B GLN* 4.4 19.5 - - - +
282B SER* 2.8 17.7 + - - +
283B ALA* 3.3 11.2 - - - +
285B HIS* 1.3 72.3 - - - +
287B GLY* 1.3 63.3 + - - +
289B ILE* 3.3 4.2 + - + +
290B ALA* 3.1 24.1 + - - +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.5 28.1 - - - +
80B GLY 3.8 7.0 - - - -
81B VAL* 3.4 14.5 - - - +
283B ALA 3.1 4.8 + - - -
284B TYR 3.1 9.2 + - - -
286B LEU* 1.3 79.1 - - - +
288B GLU* 1.3 61.7 + - - +
290B ALA* 3.4 1.6 + - - +
291B VAL* 3.3 24.3 + - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY 3.9 4.7 - - - +
83B ASP* 5.8 0.3 - - - +
84B VAL* 3.6 31.3 - - + +
284B TYR* 3.1 43.2 + - + +
285B HIS* 2.7 42.2 + - + +
287B GLY* 1.3 76.5 - - - +
289B ILE* 1.3 58.9 + - + +
291B VAL* 3.5 4.0 + - - +
292B SER* 2.8 32.6 + - - +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.7 30.5 - - + +
285B HIS* 2.8 59.9 + - + +
286B LEU* 3.9 6.5 - - + +
288B GLU* 1.3 73.1 - - + +
290B ALA* 1.3 57.9 + - - +
292B SER* 3.2 8.6 + - - +
293B GLN* 2.6 39.2 + - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 4.9 0.2 - - + -
120B ILE* 4.1 18.6 - - + -
141B VAL* 3.5 20.7 - - + +
143B ILE* 4.2 2.7 - - + -
153B ILE* 3.2 28.5 - - + +
286B LEU 3.1 12.0 + - - +
287B GLY* 3.7 6.5 - - - +
289B ILE* 1.3 78.0 - - - +
291B VAL* 1.3 58.2 + - - +
293B GLN* 3.5 2.1 + - - -
294B LEU* 2.8 30.2 + - - +
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.9 15.5 - - + -
81B VAL* 3.8 18.2 - - + +
84B VAL* 3.5 35.7 - - + -
85B ALA* 4.2 8.1 - - - +
120B ILE* 4.1 12.3 - - + +
287B GLY 3.3 16.3 + - - +
288B GLU 3.6 3.6 - - - +
290B ALA* 1.3 74.3 - - - +
292B SER* 1.3 59.6 + - - +
294B LEU* 3.9 5.6 - - - -
295B LEU* 2.9 53.6 + - + +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.1 12.5 - - - +
288B GLU* 2.8 20.3 + - - +
289B ILE* 3.5 11.5 - - - +
291B VAL* 1.3 73.4 - - - +
293B GLN* 1.3 56.8 + - - +
295B LEU* 5.0 1.1 - - - -
296B GLY* 2.7 44.2 + - - +
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Residues in contact with GLN 293 (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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141B VAL* 3.2 24.9 - - + +
151B ASN* 4.1 22.6 + - - +
152B GLY 3.1 14.8 + - - +
153B ILE* 3.1 30.5 - - + +
289B ILE* 2.6 23.9 + - + +
290B ALA 3.8 3.8 - - - +
292B SER* 1.3 72.8 - - - +
294B LEU* 1.3 61.8 + - - +
295B LEU 3.4 0.7 + - - -
296B GLY* 3.9 5.5 + - - -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.8 40.6 - - + -
117B THR 5.4 0.4 - - - +
118B GLY* 3.8 17.5 - - - -
119B MET 3.7 14.6 - - - +
120B ILE* 3.8 15.3 - - + -
139B PRO* 3.7 40.9 - - + +
140B PHE* 3.8 13.9 - - - +
141B VAL* 4.0 6.5 - - + +
290B ALA 2.8 18.9 + - - +
291B VAL* 3.5 5.4 - - - +
292B SER 3.2 0.2 - - - -
293B GLN* 1.3 79.3 - - - +
295B LEU* 1.3 62.6 + - + +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 4.1 13.7 - - + -
84B VAL* 5.8 0.4 - - + -
85B ALA* 5.5 0.2 - - - -
88B HIS* 4.6 16.2 - - + +
90B TYR* 3.6 50.0 - - + +
117B THR* 4.6 8.1 - - - +
291B VAL* 2.9 35.6 + - + +
292B SER* 4.4 0.7 - - - +
293B GLN 4.4 0.4 - - - -
294B LEU* 1.3 88.4 - - + +
296B GLY* 1.3 61.7 + - - +
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B SER* 2.7 31.9 + - - +
293B GLN* 3.9 4.1 + - - -
294B LEU 3.8 0.6 - - - -
295B LEU* 1.3 78.1 - - - +
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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