Contacts of the helix formed by residues 323 - 337 (chain B) in PDB entry 1D1T
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
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Residue Dist Surf HB Arom Phob DC
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96B GLN* 3.2 27.5 - - - +
102B ALA 3.2 8.9 + - - -
103B CYS* 2.9 30.4 + - - +
105B ASN 3.2 11.3 + - - -
106B PRO* 3.9 17.9 - - - +
108B GLY 2.8 31.8 + - - +
109B ASN* 4.4 5.9 - - + +
321B GLY 3.9 2.0 + - - +
322B LEU* 1.3 73.1 - - - +
324B SER* 1.3 55.4 + - - +
326B ASP* 3.2 14.7 + - + +
327B ASP* 2.8 42.6 + - - +
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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 18.6 - - - +
94B LEU* 2.6 49.0 + - - +
95B PRO 4.1 7.4 + - - -
96B GLN* 3.3 5.6 + - - +
319B PHE* 3.8 17.0 - - - -
322B LEU 3.5 4.2 + - - -
323B LYS* 1.3 69.8 - - - +
325B ARG* 1.3 58.7 + - - -
328B VAL* 3.0 35.9 + - - +
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 3.8 29.1 + - - +
92B LEU* 3.5 20.2 - - + -
96B GLN* 2.8 39.4 + - + +
97B CYS* 4.3 7.3 + - - +
98B ARG* 3.6 39.1 + - - +
154B GLU* 3.7 21.6 + - - +
155B SER* 3.7 22.2 + - - +
157B VAL 3.5 18.1 + - - +
158B ALA* 4.5 2.9 - - + -
324B SER* 1.3 74.7 - - - +
326B ASP* 1.3 59.0 + - - +
329B PRO* 3.3 22.5 - - - +
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Residues in contact with ASP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN* 3.1 25.1 + - - +
98B ARG* 3.0 27.1 + - - -
323B LYS* 3.6 20.1 - - + +
324B SER 3.1 0.6 - - - -
325B ARG* 1.3 80.5 - - - +
327B ASP* 1.3 71.7 + - - +
328B VAL 3.6 0.2 - - - -
329B PRO* 3.9 5.4 - - - +
330B LYS* 3.4 34.4 + - - +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 4.8 5.9 - - - +
322B LEU* 3.5 35.6 - - + +
323B LYS* 2.8 39.9 + - - +
326B ASP* 1.3 83.3 - - - +
328B VAL* 1.3 63.8 + - + +
330B LYS* 3.2 19.2 + - - +
331B LEU* 2.9 29.1 + - + +
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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* 4.0 21.8 - - + -
92B LEU* 3.8 16.4 - - + -
158B ALA* 3.7 19.5 - - + -
160B ILE* 3.9 14.4 - - + -
172B ILE* 3.9 16.1 - - + +
177B SER* 5.1 0.7 - - - +
319B PHE* 3.9 28.7 - - + -
322B LEU* 5.5 0.7 - - + -
324B SER* 3.0 21.7 + - - +
327B ASP* 1.3 75.7 - - - +
329B PRO* 1.3 67.9 - - + +
331B LEU* 3.1 13.8 + - - +
332B VAL* 3.1 13.3 + - - +
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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
----------------------------------------------------------
158B ALA* 4.0 10.3 - - + -
159B LYS 3.5 24.5 - - - +
160B ILE* 4.3 12.3 - - + -
161B ASP 5.6 0.7 + - - -
324B SER 3.9 0.2 - - - +
325B ARG 3.3 27.1 - - - +
326B ASP 3.9 3.1 - - - +
327B ASP 3.8 0.4 - - - -
328B VAL* 1.3 96.0 - - + +
330B LYS* 1.3 62.0 + - + +
332B VAL* 3.5 3.6 + - - +
333B THR* 3.1 27.3 + - - -
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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 ASP* 3.4 29.0 + - - +
327B ASP* 3.2 20.0 + - - +
328B VAL 3.1 0.8 - - - -
329B PRO* 1.3 78.1 - - + +
331B LEU* 1.3 59.5 + - + +
333B THR* 3.4 7.8 + - - -
334B GLU* 3.0 40.0 + - - +
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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* 3.9 15.7 - - + -
176B PHE* 4.2 10.3 - - + -
177B SER* 3.3 31.0 - - - +
180B TYR* 4.6 15.7 - - + -
322B LEU* 3.6 25.8 - - + -
327B ASP* 2.9 20.5 + - + +
328B VAL* 3.7 4.7 - - - +
330B LYS* 1.3 73.9 - - + +
332B VAL* 1.3 60.2 + - - +
334B GLU* 3.3 21.9 + - - +
335B PHE* 2.9 23.4 + - - +
340B PHE* 3.0 25.6 - - + -
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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* 4.1 11.9 - - + -
160B ILE* 3.5 25.6 - - + -
161B ASP* 3.9 25.4 - - + +
164B ALA* 3.7 27.1 - - + -
169B VAL* 4.5 4.9 - - + -
172B ILE* 3.9 18.8 - - + -
328B VAL 3.1 15.8 + - - +
329B PRO 3.6 9.0 - - - +
331B LEU* 1.3 76.6 - - - +
333B THR* 1.3 61.9 + - - +
335B PHE* 3.0 6.3 + - - +
336B LEU* 3.0 23.9 + - + +
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP* 5.1 7.0 + - - +
329B PRO 3.1 13.1 + - - -
330B LYS* 3.6 10.9 - - - -
331B LEU 3.3 0.2 - - - -
332B VAL* 1.3 81.1 - - - +
334B GLU* 1.3 62.0 + - + +
336B LEU* 3.3 11.9 + - + +
337B ALA* 3.0 21.7 + - + +
339B LYS* 5.5 4.0 - - - +
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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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180B TYR* 5.3 5.7 + - - -
330B LYS* 3.0 31.5 + - + +
331B LEU* 3.6 21.2 - - - +
332B VAL 3.3 0.2 - - - -
333B THR* 1.3 75.3 - - + +
335B PHE* 1.3 62.1 + - - +
337B ALA 3.3 4.7 + - - -
338B LYS 3.3 0.2 + - - -
339B LYS* 3.0 58.5 + - + +
340B PHE* 3.6 19.3 - - + -
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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
----------------------------------------------------------
165B PRO* 4.0 18.4 - - + -
168B LYS* 4.0 15.7 - - + -
169B VAL* 3.5 30.1 - - + -
172B ILE* 4.5 2.0 - - + -
331B LEU 2.9 14.5 + - - +
332B VAL* 3.2 10.3 - - - +
334B GLU* 1.3 74.0 - - - +
336B LEU* 1.3 62.8 + - + +
337B ALA 3.0 4.3 - - - -
338B LYS* 2.7 28.3 + - - +
339B LYS 4.7 0.9 - - - +
340B PHE* 3.3 35.4 - + + -
341B ASP* 4.8 0.9 - - - -
342B LEU* 3.6 40.8 - - + -
343B ASP* 4.8 4.3 - - - -
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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
----------------------------------------------------------
161B ASP* 3.8 38.6 - - + +
163B ALA* 4.2 9.6 - - + +
164B ALA* 4.0 11.9 - - + +
165B PRO* 4.0 27.1 - - + -
332B VAL* 3.0 18.2 + - + +
333B THR* 3.3 10.3 + - - +
335B PHE* 1.3 83.7 - - + +
337B ALA* 1.3 58.2 + - - +
338B LYS* 3.1 9.7 + - - +
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Residues in contact with ALA 337 (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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333B THR* 3.0 14.0 + - + +
334B GLU 3.6 1.8 - - - +
335B PHE 3.0 1.2 - - - -
336B LEU* 1.3 77.0 - - - +
338B LYS* 1.3 77.1 + - - +
339B LYS* 3.3 38.4 + - - +
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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