Contacts of the helix formed by residues 284 - 292 (chain B) in PDB entry 4WMJ
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 GLY 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 3.9 6.3 - - - -
168B PRO* 5.1 0.2 - - - -
279B LEU* 3.2 23.0 + - - -
281B SER 2.8 11.2 + - - -
283B ILE* 1.3 74.7 - - - +
285B LEU* 1.4 62.1 + - - -
286B SER 3.2 2.7 - - - -
287B ILE* 2.9 31.0 + - - +
288B SER* 3.0 10.2 + - - -
296B PHE* 3.9 6.6 - - - -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B MET* 3.6 39.6 - - + +
136B PHE* 4.0 22.9 - - + -
137B SER* 4.0 15.0 - - - +
210B ILE* 4.4 4.7 - - + -
247B VAL* 4.4 7.9 - - + -
249B LEU* 3.8 24.7 - - + -
267B PHE* 3.8 22.4 - - + -
282B ALA 2.9 17.7 + - - +
283B ILE 3.2 2.4 - - - -
284B GLY* 1.4 74.7 - - - +
286B SER* 1.3 57.6 + - - +
288B SER* 3.2 2.8 + - - -
289B LEU* 2.9 37.7 + - + +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 4.7 6.7 - - - -
158B ASN* 4.1 14.9 + - - -
168B PRO* 3.2 31.0 - - - +
172B THR* 4.2 3.3 - - - +
184B VAL* 4.2 5.2 - - - +
186B PHE* 3.6 18.4 - - - -
210B ILE* 4.1 22.6 - - - +
249B LEU* 5.5 0.6 - - - +
283B ILE 4.4 1.9 + - - -
285B LEU* 1.3 77.0 - - - +
287B ILE* 1.3 60.8 + - - +
289B LEU* 3.6 5.4 + - - +
290B TYR* 3.1 25.1 + - - +
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO* 3.9 26.7 - - + +
171B VAL* 3.9 33.2 - - + -
172B THR* 3.9 16.8 - - + -
279B LEU* 4.2 19.3 - - + +
284B GLY* 2.9 25.5 + - - +
286B SER* 1.3 72.7 + - - +
288B SER* 1.3 66.6 + - - +
290B TYR* 3.1 1.9 + - - +
291B ILE* 3.0 51.5 + - + +
296B PHE* 3.9 18.6 - - + -
299B LEU* 4.6 2.2 - - + -
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B MET* 4.3 2.6 + - - -
137B SER* 2.8 24.3 + - - -
141B ILE* 3.9 2.9 - - - +
284B GLY 3.0 8.1 + - - -
285B LEU* 3.5 14.8 - - - -
287B ILE* 1.3 79.6 - - - +
289B LEU* 1.3 57.3 + - - +
292B GLY* 2.8 33.0 + - - -
293B PHE* 3.4 28.5 + - - -
296B PHE* 4.1 23.2 - - - -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.2 11.7 - - + -
137B SER* 3.7 23.8 - - - +
140B VAL* 3.6 37.9 - - + -
141B ILE* 3.4 9.5 - - - +
156B VAL* 4.1 17.0 - - + -
180B ASN* 2.9 22.0 + - - -
182B LEU* 3.5 14.4 - - + +
184B VAL* 5.6 0.2 - - + -
208B LEU* 4.5 3.1 - - + -
210B ILE* 3.8 26.7 - - + -
285B LEU* 2.9 30.1 + - + +
286B SER* 3.8 4.9 - - - +
288B SER* 1.3 78.3 - - - +
290B TYR* 1.3 56.3 + - - +
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Residues in contact with TYR 290 (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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172B THR* 3.4 46.4 - - + -
173B GLU* 5.7 1.2 + - - -
176B LYS* 3.6 34.9 - - - +
179B ALA* 3.2 27.9 - - + +
180B ASN* 2.9 29.9 + - - +
182B LEU* 3.4 29.4 - - - -
183B LYS* 4.9 0.4 - - - -
184B VAL* 3.6 32.3 - - + -
286B SER 3.1 17.8 + - - +
287B ILE 3.1 2.9 + - - +
289B LEU* 1.3 76.6 - - - +
291B ILE* 1.3 70.5 + - + +
292B GLY 3.6 0.2 - - - -
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 5.6 1.6 - - - -
175B LEU* 3.8 53.8 - - + +
178B TYR* 3.5 23.6 - - + +
180B ASN* 4.5 3.4 - - - +
287B ILE* 3.0 34.0 + - + +
290B TYR* 1.3 96.7 - - + +
292B GLY* 1.3 61.9 + - - +
295B ASN* 2.9 51.0 + - + +
296B PHE 4.5 0.4 - - - +
299B LEU* 6.1 0.4 - - + -
487B PRO* 4.8 1.3 - - + -
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 4.0 13.9 - - - -
180B ASN* 4.1 3.8 - - - +
288B SER 2.8 18.6 + - - +
290B TYR 3.6 1.4 - - - -
291B ILE* 1.3 81.7 - - - +
293B PHE* 1.3 65.6 + - - -
294B GLU* 3.2 3.6 - - - -
295B ASN* 3.2 4.4 + - - +
296B PHE* 3.1 17.8 + - - +
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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