Contacts of the strand formed by residues 167 - 172 (chain A) in PDB entry 1YDY
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP 3.0 11.1 + - - -
61A TYR* 3.6 14.1 - - - -
62A LEU* 2.9 23.9 + - - +
155A VAL* 4.6 0.7 - - - +
165A ASN 3.9 2.2 + - - -
166A ILE* 1.3 78.9 - - - +
168A ILE* 1.3 65.1 + - - +
198A TYR* 5.8 1.1 - - - -
204A LYS* 3.2 24.9 - - - +
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Residues in contact with ILE 168 (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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61A TYR* 3.5 5.9 - - - -
62A LEU 3.4 4.0 - - - -
64A GLN* 3.6 17.0 - - - +
148A PHE* 4.4 3.1 - - + -
152A ILE* 3.2 36.8 - - + -
155A VAL* 4.2 23.1 - - + -
167A GLY* 1.3 77.3 - - - +
169A TYR* 1.3 63.5 + - - +
170A PRO* 3.5 1.3 - - + -
193A LEU* 3.6 27.8 - - + -
198A TYR* 3.7 24.7 - - + +
204A LYS 3.1 6.7 + - - +
205A VAL* 3.3 34.8 - - + -
206A TYR 3.4 2.8 + - - -
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Residues in contact with TYR 169 (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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34A ILE* 3.6 38.1 - - + -
61A TYR* 4.1 9.4 - + + -
62A LEU 2.9 16.1 + - - +
63A GLU* 3.3 17.4 - - - +
64A GLN* 3.2 4.7 + - - -
168A ILE* 1.3 73.0 - - - +
170A PRO* 1.3 61.8 - - - +
206A TYR* 3.4 46.0 - + + -
208A GLN* 3.1 48.6 + - + -
233A VAL* 3.6 16.7 - - + +
311A HIS* 2.6 30.8 + + - +
344A PHE* 3.6 19.0 - + - -
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Residues in contact with PRO 170 (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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64A GLN* 3.1 18.4 - - + +
66A LEU* 4.0 10.5 - - + -
148A PHE* 3.7 27.6 - - + -
168A ILE* 3.5 8.7 - - + +
169A TYR* 1.3 90.4 - - - +
171A GLU* 1.3 59.8 + - - +
189A THR* 5.1 0.2 - - + -
193A LEU* 4.3 4.7 - - + -
205A VAL* 3.8 15.3 - - + -
206A TYR 3.2 12.3 - - - +
207A LEU* 3.5 19.3 - - + +
208A GLN* 3.0 25.1 + - - +
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Residues in contact with GLU 171 (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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64A GLN 2.8 7.3 + - - -
65A ASP* 3.1 9.6 - - - +
66A LEU* 2.9 31.1 + - - +
170A PRO* 1.3 73.2 - - - +
172A ILE* 1.3 68.3 + - - +
173A LYS* 2.7 38.1 + - + +
208A GLN* 3.2 28.3 - - - +
209A CYS* 4.3 0.7 - - - -
210A PHE* 3.2 17.8 + - - -
235A LEU* 3.3 16.8 - - + +
902A GOL 2.9 7.6 + - - -
904A CA 2.3 31.5 - - - -
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Residues in contact with ILE 172 (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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66A LEU* 4.3 4.7 - - + -
171A GLU* 1.3 78.0 - - - +
173A LYS* 1.3 60.7 + - - +
174A ALA 3.8 0.2 + - - -
175A PRO* 3.8 16.1 - - + +
185A ILE* 3.4 37.2 - - + -
186A ALA* 3.8 18.2 - - + +
189A THR* 3.8 25.4 - - + +
207A LEU* 4.0 21.3 - - + -
208A GLN 3.2 7.5 + - - +
209A CYS* 3.5 26.5 - - + -
210A PHE 4.9 0.5 + - - -
214A GLU* 5.3 0.4 - - + -
218A ILE* 3.6 30.5 - - + -
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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