Contacts of the strand formed by residues 205 - 211 (chain D) in PDB entry 3DLX
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 GLY 205 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D THR* 3.5 13.7 - - - -
60D LEU* 3.9 21.7 - - - +
204D THR* 1.3 77.8 - - - +
206D ASP* 1.3 64.2 + - - -
207D PHE 3.4 0.4 - - - -
237D ALA 3.1 8.0 + - - +
238D ALA* 3.2 2.1 - - - +
239D GLU* 2.9 24.1 + - - +
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Residues in contact with ASP 206 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D PRO* 5.6 3.8 - - + -
56D GLY 4.5 1.0 - - - +
57D ALA* 3.2 12.5 - - + -
58D THR* 2.7 39.8 + - - +
205D GLY* 1.3 73.4 - - - -
207D PHE* 1.3 80.1 + - + +
239D GLU* 3.4 11.7 + - - +
240D THR* 2.9 24.4 + - - -
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Residues in contact with PHE 207 (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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49D ALA 5.6 0.4 - - - -
52D ASP* 3.6 37.9 - - - -
53D ILE* 3.8 38.1 - - + -
54D PRO* 3.8 22.7 - - + -
57D ALA* 4.6 0.7 - - + -
58D THR 3.2 3.2 + - - +
59D VAL* 3.3 12.3 - - + -
60D LEU* 2.8 28.6 + - - +
206D ASP* 1.3 92.0 - - + +
208D ALA* 1.3 55.5 + - - +
209D LEU* 4.9 1.8 - - + -
238D ALA* 3.4 11.1 - - - +
240D THR* 3.1 39.9 - - + +
242D VAL* 4.5 8.3 - - + -
268D ARG* 4.0 4.9 - - - -
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Residues in contact with ALA 208 (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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60D LEU* 3.2 15.5 - - + +
207D PHE* 1.3 75.3 - - - +
209D LEU* 1.3 67.1 + - - +
210D VAL* 4.0 9.4 - - + -
234D MET 3.3 29.6 - - - +
238D ALA* 3.6 11.0 - - + -
240D THR 3.0 6.5 + - - +
241D THR* 4.0 9.0 - - - +
242D VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 209 (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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50D VAL* 4.0 23.3 - - + -
53D ILE* 4.4 9.6 - - + -
59D VAL* 3.8 18.2 - - + -
60D LEU 2.7 10.9 + - - +
61D VAL* 3.6 10.6 - - + -
62D GLY 3.1 25.3 + - - -
70D PRO* 3.4 16.7 - - + +
73D LEU* 4.1 24.2 - - + +
74D ILE* 4.7 4.9 - - + +
77D LEU* 3.8 33.9 - - + -
102D LEU* 5.9 0.7 - - + -
207D PHE* 4.9 2.0 - - + -
208D ALA* 1.3 79.7 - - - +
210D VAL* 1.3 60.5 + - - +
242D VAL* 3.5 15.0 - - + -
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Residues in contact with VAL 210 (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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60D LEU 5.4 0.2 - - - +
62D GLY 5.1 0.7 - - - +
70D PRO* 4.0 3.8 - - - -
73D LEU* 4.1 0.8 - - - +
208D ALA* 4.1 15.9 - - + -
209D LEU* 1.3 79.4 - - - +
211D LYS* 1.3 64.8 + - - +
223D PHE* 4.3 4.7 - - + -
231D ASN* 3.7 32.8 - - + +
234D MET* 4.2 7.4 - - + -
235D CYS* 3.6 36.1 - - - +
241D THR* 4.7 1.8 - - + -
242D VAL 3.0 11.1 + - - +
243D VAL* 3.3 18.1 - - + -
244D GLU* 2.8 34.8 + - - +
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Residues in contact with LYS 211 (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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68D GLY* 3.9 18.6 - - - +
69D ILE 3.4 31.0 - - - +
70D PRO* 3.7 4.2 - - + +
210D VAL* 1.3 72.6 - - - +
212D ALA* 1.3 73.0 + - - +
213D TRP* 4.9 0.6 - - - +
223D PHE* 3.5 8.7 - - - -
227D ALA* 4.4 4.2 - - + +
231D ASN* 3.1 26.6 + - - -
244D GLU* 3.5 17.3 - - + +
246D GLU* 2.9 30.4 + - - -
275D TYR* 3.3 46.9 - - + +
277D LYS* 4.4 10.0 - - - +
362D ASP* 5.6 1.6 + - - -
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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