Contacts of the helix formed by residues 323 - 337 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D GLN* 3.3 30.3 - - + +
102D ALA 3.1 5.7 + - - -
103D CYS* 3.0 25.4 + - - +
105D ASN 2.8 29.8 + - - -
106D PRO* 3.9 16.8 - - - -
108D GLY 3.0 23.4 + - - +
109D ASN* 4.3 6.7 - - + +
321D GLY 4.0 1.8 + - - +
322D LEU* 1.3 70.7 - - - +
324D SER* 1.3 57.7 + - - +
326D ASP* 3.2 11.6 + - + +
327D ASP* 2.8 42.4 + - - +
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Residues in contact with SER 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 3.5 20.4 - - - -
94D LEU* 2.4 32.2 + - - +
95D PRO 3.0 18.7 + - - -
96D GLN* 3.5 2.0 + - - +
319D PHE* 4.2 16.4 - - - -
322D LEU* 3.4 5.4 + - - -
323D LYS* 1.3 69.3 - - - +
325D ARG* 1.3 61.1 + - - +
328D VAL* 3.0 42.3 + - - +
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Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D THR* 4.0 27.0 + - - +
92D LEU* 3.7 9.2 - - + -
96D GLN* 2.6 40.9 + - - +
97D CYS* 4.4 5.9 + - - +
98D ARG* 2.9 45.0 + - - +
154D GLU* 3.4 33.3 + - - +
155D SER* 3.2 25.9 - - - +
157D VAL 3.3 19.8 + - - +
158D ALA* 4.7 4.0 - - - +
324D SER* 1.3 75.7 + - - +
326D ASP* 1.3 55.4 + - - +
329D PRO* 3.3 23.2 - - - +
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Residues in contact with ASP 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLN* 2.8 27.2 + - - -
98D ARG* 2.9 26.9 + - - -
323D LYS* 3.8 13.7 - - + +
325D ARG* 1.3 78.3 - - - +
327D ASP* 1.3 68.2 + - - +
329D PRO* 4.0 4.9 - - - +
330D LYS* 3.2 34.5 - - - +
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Residues in contact with ASP 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LYS* 4.1 17.4 + - - +
321D GLY 4.9 0.2 - - - +
322D LEU* 3.5 33.1 - - + +
323D LYS* 2.8 42.8 + - - +
326D ASP* 1.3 78.6 - - - +
328D VAL* 1.3 65.0 + - - +
329D PRO 3.3 2.0 - - - -
330D LYS* 3.0 21.3 + - + +
331D LEU* 2.9 26.7 + - + +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 3.7 40.2 - - + -
92D LEU* 3.8 14.1 - - + -
158D ALA* 4.1 7.6 - - + -
160D ILE* 4.2 2.7 - - + -
172D ILE* 3.8 14.8 - - + +
319D PHE* 3.7 33.2 - - + -
322D LEU* 5.1 1.1 - - + -
324D SER* 3.0 22.6 + - - +
327D ASP* 1.3 72.0 - - - +
329D PRO* 1.4 70.7 - - + +
331D LEU* 3.2 5.4 + - - +
332D VAL* 3.0 21.3 + - - +
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Residues in contact with PRO 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ALA* 4.1 11.4 - - + -
159D LYS 3.3 27.4 - - - +
160D ILE* 4.3 11.4 - - + -
161D ASP 5.7 0.5 + - - -
324D SER 3.9 0.7 - - - +
325D ARG 3.3 24.9 - - - +
326D ASP 4.0 4.0 - - - +
327D ASP 3.7 1.6 - - - -
328D VAL* 1.4 95.2 - - + +
330D LYS* 1.3 56.6 + - + +
332D VAL* 3.4 3.2 + - + +
333D THR* 2.9 32.7 + - - +
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D ASP* 3.2 26.8 + - - +
327D ASP* 3.0 23.0 + - + +
329D PRO* 1.3 76.1 - - + +
331D LEU* 1.3 59.6 + - + +
333D THR* 3.3 7.6 + - - -
334D GLU* 2.8 42.8 + - + +
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ILE* 3.8 17.7 - - + -
176D PHE* 4.4 4.7 - - + -
177D SER* 3.3 33.4 - - - +
180D TYR* 4.1 25.8 - - + -
322D LEU* 3.6 26.7 - - + -
327D ASP* 2.9 15.4 + - + +
328D VAL 3.2 6.7 + - - +
330D LYS* 1.3 72.8 - - + +
332D VAL* 1.3 55.6 + - - +
334D GLU* 3.2 19.5 + - - +
335D PHE* 2.7 31.4 + - - +
340D PHE* 3.4 18.4 - - + -
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 4.0 16.4 - - + -
160D ILE* 3.7 24.2 - - + -
161D ASP* 4.1 24.7 - - + +
164D ALA* 3.9 26.2 - - + -
169D VAL* 4.5 7.2 - - + -
172D ILE* 4.0 13.9 - - + -
328D VAL 3.0 18.5 + - - +
329D PRO 3.6 7.9 - - - +
331D LEU* 1.3 75.3 - - - +
333D THR* 1.3 64.2 + - - +
335D PHE* 2.9 6.2 + - - +
336D LEU* 2.9 25.3 + - + +
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Residues in contact with THR 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ASP* 5.3 8.0 + - - +
329D PRO 2.9 23.3 + - - -
330D LYS* 3.6 8.5 - - - -
331D LEU 3.2 0.2 - - - -
332D VAL* 1.3 77.4 - - - +
334D GLU* 1.3 59.5 + - + +
336D LEU* 3.2 10.9 + - - +
337D ALA* 2.8 28.9 + - + +
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Residues in contact with GLU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D TYR* 4.5 9.0 + - - -
330D LYS* 2.8 30.0 + - + +
331D LEU* 3.6 22.8 - - - +
333D THR* 1.3 71.8 - - + +
335D PHE* 1.3 66.7 + - - +
337D ALA* 3.0 17.0 + - - +
339D LYS* 3.1 45.3 + - + +
340D PHE* 3.8 13.2 - - + -
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Residues in contact with PHE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PRO* 4.2 17.7 - - + -
168D LYS* 4.1 29.2 - - + -
169D VAL* 3.4 28.7 - - + -
172D ILE* 4.5 3.6 - - + -
331D LEU 2.7 17.3 + - - +
332D VAL* 3.4 9.6 - - - +
334D GLU* 1.3 72.4 - - - +
336D LEU* 1.3 69.9 + - + +
338D LYS* 2.9 22.0 + - - +
340D PHE* 3.5 37.8 - + + -
341D ASP* 4.4 6.3 - - - -
342D LEU* 3.8 32.3 - - + -
343D ASP* 6.1 0.2 - - - -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ASP* 3.4 44.4 - - + +
163D ALA* 4.2 10.8 - - + +
164D ALA* 4.2 7.2 - - - +
165D PRO* 4.0 26.5 - - + -
332D VAL* 2.9 23.0 + - + +
333D THR* 3.7 8.3 - - - +
335D PHE* 1.3 84.9 - - + +
337D ALA* 1.3 57.2 + - - +
338D LYS* 3.1 12.1 + - - +
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D THR* 2.8 18.6 + - + +
334D GLU* 3.0 12.0 + - - +
336D LEU* 1.3 76.7 - - - +
338D LYS* 1.3 71.1 + - - +
339D LYS* 3.2 22.4 + - + +
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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