Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 1DGD
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 LEU 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ALA* 3.7 34.1 - - + +
125A VAL* 4.6 14.8 - - + -
126A THR* 4.2 12.1 - - + -
205A ALA 2.9 17.6 + - - +
206A ALA* 3.2 4.6 - - + +
207A PHE* 2.9 26.0 + - - +
233A CYS* 4.4 1.0 - - - -
237A GLY 5.2 1.3 - - - +
238A MET* 1.3 79.9 - - - +
240A LEU* 1.3 61.7 + - - +
241A ILE* 3.9 3.4 - - + -
266A ASP* 3.5 21.8 - - + +
267A ILE* 4.2 13.7 - - + -
289A ILE* 4.6 22.9 - - + -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 3.6 23.1 - - + +
209A ALA* 4.9 4.3 - - + -
226A MET* 4.5 18.6 - - - -
229A LEU* 4.0 23.6 - - + -
230A LYS* 3.7 36.8 - - + +
233A CYS* 4.2 11.9 - - + -
239A LEU* 1.3 73.4 - - - +
241A ILE* 1.3 64.0 + - - +
242A LEU* 4.8 4.7 - - + -
263A VAL* 4.5 4.9 - - + -
265A PRO* 3.4 17.1 - - + +
266A ASP* 2.8 44.3 + - - +
267A ILE 3.4 3.6 + - - -
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN* 4.6 0.2 - - - +
118A ALA* 3.8 43.7 - - + +
119A ILE* 4.0 18.4 - - + -
122A ALA* 4.4 1.3 - - + -
206A ALA* 4.2 20.0 - - + -
207A PHE 2.9 13.4 + - - +
208A ILE* 3.4 24.7 - - + +
209A ALA 3.0 25.1 + - - +
239A LEU* 4.8 2.2 - - + +
240A LEU* 1.3 75.9 - - - +
242A LEU* 1.3 62.2 + - - +
267A ILE* 3.4 22.7 - - + +
269A THR* 4.1 13.9 - - + -
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA* 3.3 32.5 - - + +
210A GLU 4.5 0.4 - - - -
211A PRO* 4.3 23.1 - - + -
221A LEU* 6.0 0.2 - - + -
226A MET* 3.6 38.6 - - + -
240A LEU* 4.0 6.6 + - + -
241A ILE* 1.3 73.7 - - - +
243A ASP* 1.3 59.7 + - - +
244A GLU* 3.4 5.9 + - + +
258A CYS* 3.7 23.8 - - + -
263A VAL* 5.1 0.4 - - + +
265A PRO* 3.8 23.6 - - + -
267A ILE 3.0 8.7 + - - -
268A LEU* 3.6 8.0 - - + +
269A THR* 2.9 28.3 + - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN* 2.9 20.4 + - - +
139A HIS* 2.7 30.1 + - + +
208A ILE* 4.7 2.9 - - + -
209A ALA 2.7 16.3 + - - +
210A GLU* 3.6 8.7 - - + +
211A PRO* 3.2 18.0 - - - +
241A ILE 3.9 0.8 + - - -
242A LEU* 1.3 71.2 - - - +
244A GLU* 1.3 57.6 + - - +
245A ALA* 3.2 23.0 + - - +
246A GLN 5.3 0.3 + - - -
247A THR* 5.7 0.3 - - - +
269A THR* 3.4 12.8 + - - +
437A PLP 2.6 30.8 + - - +
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 3.7 11.9 - - + +
242A LEU* 3.4 3.5 + - + +
243A ASP* 1.3 71.5 - - - +
245A ALA* 1.3 60.1 + - - +
246A GLN 3.1 3.6 - - - -
247A THR* 2.8 21.3 + - - +
248A GLY* 2.8 40.0 + - - +
256A PHE* 3.5 11.3 - - - +
257A ALA* 2.8 35.6 + - - -
258A CYS* 2.9 22.7 + - - +
268A LEU* 3.7 18.6 - - + +
269A THR 3.0 19.5 + - - +
270A LEU* 4.2 8.6 - - + +
271A SER 4.9 0.2 + - - -
273A THR* 4.5 1.2 + - - -
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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