Contacts of the strand formed by residues 175 - 181 (chain B) in PDB entry 1YZ3
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 ALA 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B THR* 3.2 15.3 - - - +
76B ILE* 3.5 38.1 - - + +
172B PRO 3.8 4.9 + - - +
173B LEU* 3.9 0.6 - - - +
174B PRO* 1.3 73.1 - - - +
176B ASP* 1.3 63.0 + - - +
177B ALA 3.3 14.4 - - - +
178B LEU* 4.3 3.6 - - + -
204B LEU 2.8 11.8 + - - +
205B LEU* 3.4 3.1 - - - +
206B ARG* 3.1 25.3 + - - +
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER 4.4 4.8 - - - +
72B GLY* 3.6 16.8 - - - -
73B ARG* 2.7 31.1 + - - +
74B THR* 3.0 24.3 + - - +
94B PHE* 4.2 3.1 - - + -
174B PRO 4.6 3.2 - - - +
175B ALA* 1.3 74.6 - - - +
177B ALA* 1.3 60.5 + - - +
205B LEU* 3.6 1.1 - - - -
206B ARG* 2.9 33.7 + - - +
209B GLY* 3.4 24.4 - - - -
210B HIS* 3.5 3.3 + - - -
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 6.1 0.2 - - + -
70B VAL* 4.5 11.9 - - + -
74B THR 3.3 4.0 + - - +
75B LEU* 3.4 11.2 - - + -
76B ILE 3.1 22.6 + - - -
94B PHE* 3.6 30.7 - - + -
175B ALA* 3.3 3.2 - - - +
176B ASP* 1.3 81.1 - - - +
178B LEU* 1.3 70.8 + - - +
179B VAL* 5.8 0.4 - - + -
205B LEU* 3.7 2.5 - - - -
210B HIS* 3.3 12.8 - - + +
212B LEU* 6.4 0.9 - - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 5.1 0.2 - - - -
76B ILE* 3.4 29.6 - - + +
78B ILE* 4.5 6.7 - - + -
175B ALA* 4.3 9.9 - - + -
177B ALA* 1.3 84.1 - - - +
179B VAL* 1.3 66.2 + - - +
201B ILE* 3.3 47.6 - - + +
204B LEU* 4.4 13.5 - - + +
205B LEU* 4.0 22.4 - - + -
210B HIS 2.9 8.6 + - - +
211B LEU* 3.4 18.1 - - + -
212B LEU* 2.8 25.5 + - - +
248B TYR* 4.5 3.8 - - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 5.2 4.5 - - + -
65B PHE* 4.8 4.0 - - + -
75B LEU* 3.9 25.1 - - + -
76B ILE 3.0 8.4 + - - +
77B ASP* 2.9 18.4 - - - +
78B ILE* 2.8 26.2 + - - +
86B GLN* 3.9 32.1 - - + +
87B LEU* 4.3 9.6 - - + -
90B ALA* 4.9 0.4 - - + -
177B ALA* 5.8 0.9 - - + -
178B LEU* 1.3 80.4 - - - +
180B SER* 1.3 66.9 + - - +
181B ALA* 5.7 0.2 - - + -
212B LEU* 3.3 29.8 - - + +
214B ILE* 6.6 0.4 - - + -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASP* 4.1 1.3 - - - -
78B ILE* 3.0 37.5 + - - +
179B VAL* 1.3 79.2 - - - +
181B ALA* 1.3 60.4 + - - +
183B CYS* 3.7 14.0 - - - +
184B LEU* 4.7 3.5 - - - +
201B ILE* 5.0 3.8 - - - -
211B LEU* 4.9 5.6 - - - -
212B LEU 2.8 9.7 + - - +
213B LEU* 3.3 26.4 - - - +
214B ILE* 2.9 22.7 + - - -
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASP* 4.7 3.0 + - - -
78B ILE 4.2 2.6 + - - -
79B GLY 3.9 1.9 - - - +
85B TYR* 3.5 26.7 - - + +
86B GLN* 4.5 13.9 - - + -
179B VAL* 5.7 0.4 - - + -
180B SER* 1.3 76.5 + - - +
182B PHE* 1.3 68.4 + - + +
183B CYS* 3.1 3.8 + - - -
214B ILE* 3.4 20.9 - - + -
2001B SAH 2.8 34.0 + - - +
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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