Contacts of the strand formed by residues 194 - 200 (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 LEU 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D VAL* 3.7 28.9 - - + +
190D THR* 3.1 6.4 - - - -
191D PHE 2.9 32.4 + - - +
192D LYS 3.2 10.2 - - - +
193D ASP* 1.3 87.7 - - + +
195D HIS* 1.3 64.9 + - - +
196D PHE* 3.6 23.1 - - + -
340D THR* 4.6 3.4 - - + -
343D ILE* 4.4 9.6 - - + -
344D ILE* 3.4 29.8 - - + -
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Residues in contact with HIS 195 (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 3.0 26.6 + - - +
189D PHE 3.8 4.3 - - - -
190D THR* 3.6 26.4 + - + +
193D ASP 4.2 6.2 + - - -
194D LEU* 1.3 80.0 - - - +
196D PHE* 1.3 61.0 + - - +
197D LYS* 4.0 25.9 + - - +
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Residues in contact with PHE 196 (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* 3.7 13.9 - - + -
36D LEU* 4.1 23.8 - - + -
188D HIS* 3.3 26.2 - - - +
189D PHE* 2.8 55.6 + + + +
191D PHE* 3.7 20.6 - - + -
194D LEU* 3.6 39.0 - - + -
195D HIS* 1.3 73.9 - - - +
197D LYS* 1.3 66.8 + - - +
198D MET* 3.9 1.1 - - + +
336D PHE* 4.0 14.1 - + - -
340D THR* 3.7 22.0 - - + -
343D ILE* 4.3 14.6 - - + -
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Residues in contact with LYS 197 (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 3.2 15.0 + - - +
35D LYS* 3.9 6.5 - - + -
36D LEU* 3.1 26.3 + - - +
186D GLU* 4.2 1.3 - - - +
188D HIS* 3.0 46.6 + - + +
195D HIS* 4.1 30.9 + - - +
196D PHE* 1.3 75.6 + - - +
198D MET* 1.3 60.2 + - - +
199D PHE* 3.9 21.1 - - + -
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Residues in contact with MET 198 (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* 3.6 22.7 - - + +
37D LEU 5.5 0.2 - - - -
38D LEU* 3.9 33.4 - - + -
49D ILE* 4.7 6.1 - - + -
50D VAL* 4.7 6.0 - - + +
53D MET* 3.9 26.9 - - + -
185D VAL 3.6 0.7 - - - +
186D GLU* 3.1 6.8 - - - +
187D THR* 2.9 56.4 + - + +
189D PHE* 4.3 8.5 - - + -
196D PHE* 5.4 0.9 - - + -
197D LYS* 1.3 72.5 - - - +
199D PHE* 1.3 65.7 + - - +
200D ASP 4.1 0.8 + - - +
222D ILE* 4.8 9.0 - - + -
336D PHE* 3.8 32.5 - - + -
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Residues in contact with PHE 199 (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* 4.3 21.8 - - + -
36D LEU 3.1 15.0 + - - -
37D LEU* 3.7 21.7 - - + -
38D LEU* 2.9 29.9 + - - -
184D ILE* 4.0 21.1 - - + -
185D VAL 3.3 1.8 - - - +
186D GLU* 3.0 51.1 - - + -
197D LYS* 3.9 20.6 - - + -
198D MET* 1.3 72.4 - - - +
200D ASP* 1.3 62.0 + - - +
201D VAL* 3.3 6.9 + - + +
214D CYS* 5.7 3.4 - - - -
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Residues in contact with ASP 200 (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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38D LEU* 3.9 7.6 - - + -
46D LYS* 3.3 37.2 - - - +
47D SER* 3.4 31.5 + - - -
50D VAL* 3.8 14.5 - - + +
181D THR* 4.7 8.9 + - - +
183D GLY 4.3 1.6 - - - +
184D ILE* 3.3 8.0 - - - +
185D VAL* 2.7 48.2 + - + +
198D MET* 4.1 2.0 + - - +
199D PHE* 1.3 68.3 - - - +
201D VAL* 1.3 63.6 + - - +
202D GLY* 3.9 0.9 + - - -
358D GDP 4.6 0.5 + - - -
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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