Contacts of the helix formed by residues 310 - 322 (chain B) in PDB entry 1DCT
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 VAL 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLY* 5.0 2.5 - - - +
15B LEU* 4.0 44.6 - - + -
16B GLY* 4.1 2.2 - - - +
19B LYS* 3.5 31.4 - - - +
284B GLN 3.2 5.5 + - - +
285B GLY* 2.8 35.4 - - - +
286B PHE* 4.1 6.7 - - + +
287B PRO* 4.5 2.7 - - + -
308B VAL 3.3 4.5 + - - +
309B PRO* 1.3 73.3 - - - +
311B ASN* 1.3 66.9 + - - +
313B ALA* 2.8 13.6 + - - +
314B TYR 2.8 11.1 + - - -
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Residues in contact with ASN 311 (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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19B LYS* 3.7 11.1 + - - +
147B TYR 2.9 25.0 + - - +
148B GLY* 4.2 16.7 - - - +
149B VAL* 4.3 4.9 - - + +
175B HIS* 4.2 4.8 + - - -
285B GLY* 5.8 1.2 - - - -
309B PRO* 3.6 1.0 - - - +
310B VAL* 1.3 78.4 - - - +
312B LEU* 1.3 54.2 + - - +
314B TYR* 3.0 25.1 + - - +
315B GLU* 2.6 59.9 + - - +
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Residues in contact with LEU 312 (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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142B LEU* 4.2 11.7 - - + +
143B ASN 4.7 0.4 - - - -
144B ALA* 3.6 28.3 - - + +
147B TYR* 4.0 34.5 - - + -
149B VAL* 3.8 14.7 - - + +
153B ARG* 4.6 4.5 - - + +
155B ARG* 5.1 6.7 - - + -
157B PHE* 4.2 22.9 - - + -
308B VAL* 5.1 1.8 - - + -
309B PRO* 3.3 27.1 + - + +
310B VAL 3.3 0.6 - - - -
311B ASN* 1.3 76.3 - - - +
313B ALA* 1.3 65.6 + - - +
315B GLU* 3.4 1.1 + - + +
316B ILE* 3.1 36.7 + - + +
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Residues in contact with ALA 313 (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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12B GLY 4.7 0.2 - - - +
13B LEU* 4.0 22.2 - - + +
16B GLY* 4.0 12.8 - - - +
17B PHE* 4.8 1.8 - - + -
308B VAL* 3.2 28.7 - - + +
309B PRO 3.1 5.3 + - - +
310B VAL* 2.8 10.9 + - - +
312B LEU* 1.3 76.5 - - - +
314B TYR* 1.3 65.3 + - - +
316B ILE* 2.7 23.3 + - - +
317B ALA* 2.8 14.5 + - - +
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Residues in contact with TYR 314 (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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16B GLY* 3.6 22.3 - - - -
19B LYS* 3.5 56.1 + - + +
20B ALA* 3.6 7.9 - - + -
310B VAL 2.8 14.4 + - - +
311B ASN* 3.2 32.1 - - - +
313B ALA* 1.3 72.2 - - - +
315B GLU* 1.3 65.7 + - - +
317B ALA* 3.3 2.3 - - - +
318B LYS* 3.0 66.8 + - + +
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Residues in contact with GLU 315 (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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147B TYR* 3.7 29.2 - - + +
172B PRO* 4.3 12.5 - - + +
173B ILE 5.5 1.6 - - - +
175B HIS* 3.3 23.4 + - + -
311B ASN* 2.6 47.3 + - - +
312B LEU 3.6 5.4 - - - +
313B ALA 2.8 2.8 + - - -
314B TYR* 1.3 80.6 - - - +
316B ILE* 1.3 65.9 + - + +
318B LYS* 3.1 30.0 + - - +
319B THR* 3.5 10.2 + - - +
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Residues in contact with ILE 316 (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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13B LEU* 6.2 1.1 - - + -
17B PHE* 5.3 2.0 - - + -
107B LEU* 3.6 14.8 - - + -
140B ILE* 4.8 1.1 - - + -
142B LEU* 4.2 12.3 - - + -
157B PHE* 3.1 50.3 - - + -
159B ILE* 3.6 29.6 - - + -
169B TYR* 4.3 4.3 - - - +
172B PRO* 4.7 7.2 - - + -
312B LEU* 3.1 26.0 - - + +
313B ALA* 2.7 13.8 + - - +
315B GLU* 1.3 72.4 - - - +
317B ALA* 1.3 61.6 + - - +
319B THR* 2.6 26.7 + - - -
320B ILE* 3.4 7.1 + - + +
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Residues in contact with ALA 317 (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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17B PHE* 3.8 52.4 - - + -
20B ALA* 4.1 8.3 - - + -
22B PHE* 3.6 10.7 - - + -
313B ALA 2.8 10.9 + - - +
314B TYR* 3.3 13.2 - - - +
316B ILE* 1.3 78.6 - - - +
318B LYS* 1.3 63.2 + - - +
319B THR 3.2 0.5 + - - -
320B ILE* 3.3 2.2 + - - +
321B LYS* 3.1 18.2 + - - +
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Residues in contact with LYS 318 (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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20B ALA* 4.0 7.6 - - + -
314B TYR* 3.0 65.1 + - + +
315B GLU* 3.1 20.4 + - - +
317B ALA* 1.3 75.9 - - - +
319B THR* 1.3 62.5 + - + +
321B LYS* 3.5 8.4 + - + +
322B SER* 3.0 24.4 + - - -
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Residues in contact with THR 319 (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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169B TYR* 3.0 22.3 + - - -
170B LEU 3.1 27.8 - - - +
171B PRO 3.8 2.0 - - - +
172B PRO* 3.6 34.3 - - + -
315B GLU 4.0 3.8 - - - +
316B ILE 2.6 19.4 + - - -
318B LYS* 1.3 74.1 - - + +
320B ILE* 1.3 69.6 + - - +
322B SER* 2.7 23.9 + - - +
323B ALA* 2.8 12.3 + - - +
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Residues in contact with ILE 320 (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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17B PHE* 4.2 12.3 - - + -
22B PHE* 4.1 5.2 - - + -
105B PHE* 3.6 45.3 - - + -
107B LEU* 3.7 30.1 - - + -
159B ILE* 3.9 23.3 - - + -
161B PHE* 4.0 6.3 - - + -
169B TYR* 4.1 9.9 - - + -
316B ILE 3.9 9.2 - - - +
317B ALA 3.3 6.8 + - - +
319B THR* 1.3 82.0 + - - +
321B LYS* 1.3 62.6 + - - +
323B ALA* 3.2 12.8 + - - +
324B LEU* 3.0 35.3 - - + +
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Residues in contact with LYS 321 (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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1B MET* 5.7 1.8 - - + -
20B ALA* 3.3 34.9 + - + +
21B GLY* 4.5 7.0 - - - -
22B PHE* 3.7 18.6 - - + -
317B ALA 3.1 12.6 + - - +
318B LYS* 3.5 11.7 - - - +
319B THR 3.0 0.4 - - - -
320B ILE* 1.3 77.4 - - - +
322B SER* 1.3 58.2 + - - +
324B LEU* 2.9 31.3 + - - +
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Residues in contact with SER 322 (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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318B LYS 3.0 15.0 + - - -
319B THR* 2.7 27.3 + - - +
321B LYS* 1.3 74.5 - - - +
323B ALA* 1.3 57.1 + - - +
324B LEU* 3.0 9.1 + - - +
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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