Contacts of the helix formed by residues 323 - 336 (chain B) in PDB entry 1U3T
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 LYS 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLN* 3.5 30.0 - - - +
102B ILE 3.4 4.2 + - - -
103B CYS* 3.0 27.4 + - - +
105B ASN 2.7 28.0 + - - -
106B PRO* 3.8 20.4 - - - -
108B SER 2.8 25.5 + - - +
109B ASN* 3.8 10.5 - - + +
321B GLY 3.7 2.5 + - - +
322B PHE* 1.3 68.3 - - - +
324B SER* 1.3 58.0 + - - +
326B GLU* 3.8 24.0 - - - +
327B CYS* 2.8 39.1 + - - +
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Residues in contact with SER 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.7 18.0 - - - +
94B ILE* 2.6 31.2 + - - +
95B PRO 3.5 16.6 + - - -
96B GLN* 3.6 2.6 + - - +
109B ASN* 5.1 2.0 + - - +
319B LEU* 3.8 20.9 - - - -
322B PHE* 3.0 7.6 + - - -
323B LYS* 1.3 70.7 - - - +
325B LYS* 1.3 60.8 + - - +
328B VAL* 2.9 38.4 + - - +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 3.3 36.6 + - - -
83B VAL* 5.0 1.0 - - - +
92B LEU* 3.3 14.1 - - + +
96B GLN* 3.1 26.1 + - + +
154B GLU* 3.0 18.1 + - - -
155B ASN* 4.0 18.8 - - - +
157B VAL* 2.4 38.0 + - - +
158B ALA* 3.7 8.6 - - + +
159B LYS 5.4 0.2 - - - +
324B SER* 1.3 79.3 + - - +
326B GLU* 1.3 56.3 + - - +
329B PRO* 3.1 24.3 - - - +
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Residues in contact with GLU 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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96B GLN* 3.1 27.8 + - - +
323B LYS* 3.8 24.1 - - - +
325B LYS* 1.3 79.3 - - + +
327B CYS* 1.3 68.9 + - - +
329B PRO* 3.7 7.6 - - - +
330B LYS* 3.9 30.8 + - - +
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Residues in contact with CYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 3.8 36.6 - - + -
323B LYS* 2.8 33.8 + - - +
326B GLU* 1.3 89.4 - - - +
328B VAL* 1.3 57.7 + - - +
329B PRO 3.3 2.7 - - - -
330B LYS* 2.9 20.0 + - + +
331B LEU* 2.8 33.1 + - + +
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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
----------------------------------------------------------
90B ILE* 3.6 42.2 - - + -
92B LEU* 3.8 18.4 - - + -
158B ALA* 4.6 1.6 - - + -
160B ILE* 4.5 3.8 - - + -
172B ILE* 4.0 24.9 - - + +
173B GLY* 5.1 2.2 - - - +
177B SER* 5.1 2.5 - - - +
319B LEU* 5.0 8.3 - - + -
322B PHE* 6.2 2.0 - - + -
324B SER* 2.9 27.6 + - - +
327B CYS* 1.3 76.8 - - + +
329B PRO* 1.3 67.0 - - + +
331B LEU* 3.2 6.6 + - + +
332B VAL* 3.0 21.7 + - - +
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Residues in contact with PRO 329 (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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158B ALA* 3.6 12.3 - - + -
159B LYS 3.5 25.1 - - - +
160B ILE* 4.3 14.1 - - + -
161B ASP 5.7 0.9 + - - -
325B LYS 3.1 26.5 - - - +
326B GLU 3.7 5.2 - - - +
327B CYS 3.5 2.5 - - - -
328B VAL* 1.3 95.8 - - + +
330B LYS* 1.3 56.1 + - - +
332B VAL* 3.4 4.2 + - + +
333B ALA* 2.9 27.4 + - - +
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLU* 3.9 36.2 + - - +
327B CYS* 2.9 24.1 + - - +
329B PRO* 1.3 79.0 - - - +
331B LEU* 1.3 57.1 + - + +
333B ALA* 3.3 7.8 + - + +
334B ASP* 2.7 43.2 + - - +
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Residues in contact with LEU 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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172B ILE* 3.7 16.4 - - + -
176B PHE* 4.7 8.3 - - + -
177B SER* 3.1 35.4 - - - +
180B TYR* 5.1 7.0 - - + -
322B PHE* 4.1 37.2 - - + -
327B CYS* 2.8 19.1 + - + +
328B VAL* 3.2 8.9 + - + +
330B LYS* 1.3 74.3 - - + +
332B VAL* 1.3 60.7 + - - +
334B ASP* 3.1 6.8 + - + +
335B PHE* 3.0 22.9 + - - +
340B PHE* 3.3 28.5 - - + -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.7 27.1 - - + -
160B ILE* 4.1 14.1 - - + -
161B ASP* 4.3 13.2 - - + +
164B SER* 3.2 26.7 - - - +
169B VAL* 4.3 13.5 - - + -
172B ILE* 3.8 18.4 - - + -
328B VAL 3.0 17.5 + - - +
329B PRO* 3.6 9.6 - - + +
331B LEU* 1.3 77.4 - - - +
333B ALA* 1.3 55.3 + - - +
335B PHE* 3.1 3.4 + - - +
336B MET* 3.0 29.8 + - + +
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Residues in contact with ALA 333 (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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161B ASP* 5.7 5.4 - - + +
329B PRO 2.9 17.7 + - - +
330B LYS* 3.5 11.4 - - + +
331B LEU 3.2 0.2 - - - -
332B VAL* 1.3 76.5 - - - +
334B ASP* 1.3 63.1 + - - +
335B PHE 3.3 0.2 - - - -
336B MET* 3.7 7.8 + - - +
337B ALA* 3.4 21.1 + - - +
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Residues in contact with ASP 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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330B LYS* 2.7 32.9 + - - +
331B LEU* 3.1 12.5 + - + +
333B ALA* 1.3 80.8 - - - +
335B PHE* 1.3 61.3 + - - +
337B ALA* 3.3 8.3 + - - -
339B LYS* 2.9 70.0 + - + +
340B PHE* 3.9 10.5 - - + -
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Residues in contact with PHE 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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165B PRO* 3.6 26.0 - - + -
168B LYS* 3.5 30.7 - - + -
169B VAL* 3.7 21.5 - - + -
172B ILE* 4.3 2.5 - - + -
331B LEU 3.0 11.7 + - - +
332B VAL* 3.1 11.9 + - - +
334B ASP* 1.3 76.7 - - - +
336B MET* 1.3 66.2 + - - +
338B LYS* 2.8 27.4 + - - +
340B PHE* 3.2 45.4 - + + +
341B SER* 4.1 2.0 - - - -
342B LEU* 3.7 30.3 - - + -
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Residues in contact with MET 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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161B ASP* 3.9 20.2 - - + +
163B ALA* 2.9 38.1 - - + +
164B SER* 4.3 4.7 - - - +
165B PRO* 3.8 23.6 - - + -
332B VAL* 3.0 28.5 + - + +
333B ALA* 4.0 7.4 - - - +
334B ASP 3.3 0.2 - - - -
335B PHE* 1.3 84.1 - - - +
337B ALA* 1.3 55.5 + - - +
338B LYS* 3.2 16.2 + - - -
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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