Contacts of the strand formed by residues 35 - 40 (chain D) in PDB entry 1Y3A
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 35 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D VAL* 1.3 73.6 - - - +
36D LEU* 1.3 69.2 + - - +
37D LEU* 5.0 1.6 - - + -
197D LYS* 3.9 11.2 - - + +
199D PHE* 4.3 25.1 - - + -
213D HIS 3.2 20.0 + - - -
214D CYS* 3.2 17.6 + - - +
216D GLU* 2.7 21.9 + - - +
217D GLY 3.2 26.2 - - - +
218D VAL* 3.8 8.1 - - + +
219D THR* 3.1 27.5 + - - +
220D ALA 3.5 4.3 + - - +
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Residues in contact with LEU 36 (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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34D VAL* 3.3 34.3 + - + -
35D LYS* 1.3 76.9 - - - +
37D LEU* 1.3 69.1 + - - +
196D PHE* 4.1 22.7 - - + -
197D LYS 3.1 13.9 + - - +
198D MET* 4.3 16.6 - - + -
199D PHE* 3.1 25.1 + - - -
218D VAL* 5.0 0.2 - - - -
220D ALA* 3.3 19.1 - - + +
222D ILE* 4.2 16.8 - - + -
336D PHE* 4.1 22.4 - - + -
339D VAL* 5.0 2.7 - - + -
343D ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 37 (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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35D LYS* 5.0 2.7 - - + -
36D LEU* 1.3 84.3 - - - +
38D LEU* 1.3 61.1 + - - +
39D LEU* 4.0 6.3 - - + -
198D MET* 5.5 0.2 - - - -
199D PHE* 3.7 26.7 - - + -
201D VAL* 4.3 11.4 - - + -
214D CYS* 4.0 17.0 - - - +
215D PHE* 3.4 39.9 - - + -
218D VAL* 3.9 22.7 - - + -
220D ALA 3.2 5.7 + - - -
221D ILE* 3.4 24.5 - - + +
222D ILE* 2.8 30.1 + - - +
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Residues in contact with LEU 38 (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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36D LEU 4.2 0.2 - - - -
37D LEU* 1.3 73.8 - - - +
39D LEU* 1.3 62.6 + - - +
46D LYS* 3.5 42.1 - - + +
49D ILE* 4.2 16.4 - - + -
50D VAL* 3.8 17.7 - - + -
198D MET* 3.9 21.3 - - + -
199D PHE 2.9 17.3 + - - +
200D ASP* 4.0 5.8 - - + -
201D VAL 3.0 26.0 + - - +
222D ILE* 3.6 39.9 - - + +
224D CYS* 4.4 8.7 - - - -
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Residues in contact with LEU 39 (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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37D LEU* 4.7 8.7 - - + -
38D LEU* 1.3 77.3 - - - +
40D GLY* 1.3 54.0 + - - +
46D LYS* 3.6 8.1 - - - +
201D VAL* 3.4 43.1 - - + +
215D PHE* 5.0 8.3 - - + -
221D ILE* 3.7 26.9 - - + -
222D ILE 2.8 11.2 + - - +
223D PHE* 3.8 13.0 - - + -
224D CYS* 2.7 35.5 + - - +
253D ILE* 3.5 32.1 - - + -
5H TRP* 4.0 21.5 - - + +
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Residues in contact with GLY 40 (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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39D LEU* 1.3 78.3 - - - +
41D ALA* 1.3 69.9 + - - +
42D GLY 3.7 0.2 + - - -
44D SER* 3.7 4.3 - - - -
46D LYS* 3.3 14.4 + - - +
201D VAL 4.7 2.9 + - - +
202D GLY* 5.4 2.9 - - - -
223D PHE* 3.5 19.3 - - - -
224D CYS 3.5 10.8 - - - -
249D LEU* 4.7 3.6 - - - -
5H TRP* 4.8 6.6 + - - -
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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