Contacts of the helix formed by residues 322 - 338 (chain B) in PDB entry 4XJO
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 ASN 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A TYR 3.1 21.4 + - - -
290A LEU* 3.8 11.5 - - - +
291A SER* 5.3 2.4 + - - +
88B ASN 3.4 12.3 + - - -
89B HIS* 3.0 27.5 + - + +
122B ASP* 5.2 2.7 - - - +
292B LEU* 5.0 3.7 - - + +
319B PHE* 3.0 25.1 + - + +
320B MET 3.2 0.2 - - - -
321B ALA* 1.3 75.9 - - - +
323B PRO* 1.4 64.8 - - - +
324B LEU* 3.3 7.9 + - - +
325B ALA* 2.9 33.3 + - + +
326B CYS* 2.9 27.8 + - - +
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Residues in contact with PRO 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLN* 3.7 14.0 - - - +
87B MET* 3.6 38.6 - - + +
88B ASN 3.6 1.1 - - - +
89B HIS* 3.5 31.4 - - + +
90B VAL 4.0 2.9 - - - +
97B HIS* 3.6 25.6 - - + +
99B PRO* 3.7 7.2 - - + +
321B ALA 3.4 8.1 - - - +
322B ASN* 1.4 82.3 - - - +
324B LEU* 1.3 56.1 + - - +
327B ALA* 2.9 32.2 + - - +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.1 19.3 - - + -
289A TYR* 3.6 23.3 - - + +
290A LEU* 3.9 14.4 - - + -
80B LEU* 3.7 25.3 - - + +
83B GLN* 3.9 11.7 - - + -
84B LEU* 3.7 37.9 - - + +
88B ASN* 3.3 27.3 + - + +
290B LEU* 4.1 2.9 - - - -
322B ASN* 3.3 8.3 + - - +
323B PRO* 1.3 78.1 - - - +
325B ALA* 1.3 63.8 + - - +
327B ALA* 3.3 2.1 + - - +
328B VAL* 3.1 23.9 + - - +
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Residues in contact with ALA 325 (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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290A LEU* 5.5 0.4 - - + -
286B THR* 4.4 0.4 - - + -
290B LEU* 3.8 21.2 - - + +
291B SER 4.1 20.0 - - - +
292B LEU* 4.0 18.8 - - + -
322B ASN* 2.9 23.6 + - + +
324B LEU* 1.3 74.3 - - - +
326B CYS* 1.3 58.3 + - - +
328B VAL* 3.3 5.9 - - - +
329B SER* 2.8 33.2 + - - -
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Residues in contact with CYS 326 (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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99B PRO* 3.7 27.4 - - + +
100B ALA* 4.2 12.1 - - - +
103B LEU* 3.9 22.5 - - + +
120B PHE* 4.5 6.5 - - - -
292B LEU* 4.2 9.0 - - - -
321B ALA* 3.7 26.0 - - - -
322B ASN 2.9 21.7 + - - +
325B ALA* 1.3 76.6 - - - +
327B ALA* 1.3 56.6 + - - +
329B SER* 3.3 2.1 + - - -
330B VAL* 2.9 33.6 + - - +
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Residues in contact with ALA 327 (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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79B ALA* 4.0 12.3 - - + +
80B LEU* 5.5 0.4 - - - +
83B GLN* 3.6 32.8 - - + +
99B PRO* 4.0 7.4 - - + +
323B PRO 2.9 18.1 + - - +
324B LEU 3.3 4.5 + - - +
326B CYS* 1.3 77.7 - - - +
328B VAL* 1.3 61.8 + - - +
330B VAL* 3.4 8.0 + - - +
331B ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.6 38.8 - - + +
79B ALA* 4.3 7.1 - - - +
80B LEU* 4.8 10.8 - - + -
286B THR* 3.7 23.8 - - - +
289B TYR* 4.0 20.2 - - + -
290B LEU* 4.2 11.9 - - + -
324B LEU 3.1 12.9 + - - +
325B ALA* 3.3 15.0 - - - +
327B ALA* 1.3 76.3 - - - +
329B SER* 1.3 63.1 + - - +
331B ALA* 3.3 2.3 + - - +
332B SER* 2.8 28.2 + - - -
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.5 23.3 - - - -
285B LEU* 3.3 19.8 + - - -
286B THR* 2.9 23.3 - - - +
292B LEU* 3.2 8.2 - - - +
325B ALA 2.8 20.7 + - - -
326B CYS 3.4 5.2 - - - -
328B VAL* 1.3 75.2 - - - +
330B VAL* 1.3 59.1 + - - +
332B SER* 3.1 1.4 + - - -
333B VAL* 2.8 35.2 + - - +
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PRO* 4.0 4.9 - - + +
102B ARG* 3.6 46.2 - - + +
103B LEU* 3.7 35.6 - - + +
106B LEU* 3.9 9.6 - - + -
326B CYS 2.9 19.5 + - - +
327B ALA* 3.6 10.8 - - - +
329B SER* 1.3 74.2 - - - +
331B ALA* 1.3 58.4 + - - +
333B VAL* 3.4 0.9 + - - +
334B GLU* 2.9 37.9 + - - +
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Residues in contact with ALA 331 (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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75B ALA* 4.3 6.8 - - + +
76B LEU* 3.6 14.0 - - + +
79B ALA* 3.4 33.2 - - + -
327B ALA 3.2 3.2 + - - +
328B VAL 3.5 6.7 - - - +
330B VAL* 1.3 81.6 - - - +
332B SER* 1.3 55.7 + - - +
334B GLU* 3.5 7.7 + - - +
335B LEU* 2.9 30.8 + - - +
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 4.0 5.9 - - - +
69B HIS* 2.9 43.9 + - - -
76B LEU* 3.5 13.0 - - - +
284B ALA 4.1 2.1 + - - -
285B LEU 4.1 3.1 - - - -
286B THR 4.0 3.1 - - - -
287B GLY* 3.4 27.6 + - - -
328B VAL 2.8 16.5 + - - -
329B SER 3.6 4.5 - - - -
331B ALA* 1.3 75.6 - - - +
333B VAL* 1.3 63.4 + - - +
335B LEU* 3.4 0.7 + - - -
336B LEU* 3.1 11.6 + - - +
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.5 11.4 - - + -
106B LEU* 4.3 19.1 - - + -
107B LEU* 4.9 1.6 - - + -
110B ILE* 3.8 25.8 - - + -
260B PHE* 3.8 30.3 - - + -
285B LEU* 4.4 9.2 - - + +
329B SER 2.8 25.5 + - - +
330B VAL 3.9 2.7 - - - +
332B SER* 1.3 72.3 - - - +
334B GLU* 1.3 57.5 + - - +
336B LEU* 3.2 8.0 + - + +
337B LEU* 3.0 42.0 + - + +
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Residues in contact with GLU 334 (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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102B ARG* 2.8 44.0 + - - -
106B LEU* 4.0 18.0 - - + +
330B VAL* 2.9 27.1 + - - +
331B ALA* 3.9 5.9 - - - +
333B VAL* 1.3 75.6 - - - +
335B LEU* 1.3 57.7 + - - +
337B LEU* 3.8 6.8 - - + +
338B GLY* 2.9 28.4 + - - -
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Residues in contact with LEU 335 (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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69B HIS* 3.5 33.2 - - + +
73B HIS* 3.5 45.1 - - + +
75B ALA* 4.7 8.1 - - + -
76B LEU* 4.0 10.5 - - + -
331B ALA 2.9 17.5 + - - +
332B SER 3.6 3.8 - - - +
333B VAL 3.3 0.2 - - - -
334B GLU* 1.3 78.4 - - - +
336B LEU* 1.3 60.2 + - - +
338B GLY* 3.6 6.2 + - - -
339B GLN* 3.0 29.2 + - - +
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Residues in contact with LEU 336 (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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68B ILE* 4.9 3.1 - - + -
69B HIS* 3.7 14.5 - - + +
260B PHE* 3.5 43.1 - - + +
261B GLY* 4.9 1.6 - - - -
266B LEU* 3.8 19.1 - - + -
332B SER 3.1 14.0 + - - +
333B VAL* 3.6 10.8 - - + +
335B LEU* 1.3 77.0 - - - +
337B LEU* 1.3 62.0 + - + +
339B GLN* 3.4 19.5 - - - +
341B TRP* 3.3 43.7 - - + -
412B TYR* 3.8 30.7 - - + -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.1 14.1 - - + -
110B ILE* 3.7 25.6 - - + -
266B LEU* 4.0 35.9 - - + -
333B VAL* 3.0 35.4 + - + +
334B GLU* 4.1 5.6 - - + +
336B LEU* 1.3 78.1 - - + +
338B GLY* 1.3 58.9 + - - +
339B GLN 3.2 8.2 + - - +
341B TRP* 4.3 12.7 + - - +
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Residues in contact with GLY 338 (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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334B GLU 2.9 17.6 + - - -
335B LEU* 3.6 3.5 + - - -
336B LEU 3.3 0.4 - - - -
337B LEU* 1.3 75.9 - - - +
339B GLN* 1.3 57.7 + - - +
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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