Contacts of the strand formed by residues 170 - 175 (chain B) in PDB entry 1H5Y
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 GLU 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 2.6 38.3 + - - -
102B LYS* 2.6 33.0 + - - +
126B GLN 5.8 2.5 - - - +
128B THR 3.6 1.9 + - - +
129B VAL* 3.5 21.4 - - + +
130B VAL 3.1 23.9 + - - -
168B ALA* 3.4 4.4 - - - +
169B GLY* 1.3 83.0 - - - +
171B ILE* 1.3 66.6 + - - +
199B ILE* 3.7 4.3 - - - +
200B PRO* 3.5 21.2 - - + +
202B ILE* 3.5 25.6 - - + +
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Residues in contact with ILE 171 (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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130B VAL 3.4 10.8 - - - +
132B ILE* 3.9 16.4 - - + -
160B ALA* 3.5 38.4 - - + +
163B VAL* 4.5 10.1 - - + -
170B GLU* 1.3 79.1 - - - +
172B LEU* 1.3 64.6 + - - +
173B LEU* 4.1 13.2 - - + +
193B VAL* 4.2 9.2 - - + -
197B VAL* 4.1 15.7 - - + -
199B ILE* 3.8 20.2 - - + +
200B PRO 3.1 6.5 + - - -
201B VAL* 3.4 8.9 - - + -
202B ILE* 2.7 35.0 + - - +
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Residues in contact with LEU 172 (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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51B ALA* 5.4 1.3 - - + -
53B LEU* 4.8 16.4 - - + -
81B LEU* 4.4 26.7 - - + -
104B SER* 4.7 3.6 - - - +
129B VAL* 4.0 10.7 - - + +
130B VAL 3.0 6.5 + - - -
131B ALA* 3.2 20.5 - - + +
132B ILE 2.8 32.6 + - - +
133B ASP* 5.3 0.2 - - - +
170B GLU 4.2 0.6 - - - -
171B ILE* 1.3 69.9 - - - +
173B LEU* 1.3 53.0 + - - +
174B THR* 3.5 21.9 + - - +
202B ILE* 3.7 16.2 - - + +
204B SER* 3.8 17.9 - - - +
225B LEU* 3.8 20.2 - - + -
401B GOL 4.6 9.0 - - - -
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Residues in contact with LEU 173 (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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132B ILE* 3.5 28.5 - - + +
134B ALA* 5.0 1.8 - - + -
156B ALA* 5.2 0.2 - - + -
171B ILE* 4.1 5.4 - - + -
172B LEU* 1.3 72.1 - - - +
174B THR* 1.3 59.7 + - - +
189B LEU* 3.8 28.0 - - + +
190B ILE* 3.8 29.9 - - + +
193B VAL* 3.7 42.6 - - + -
201B VAL* 3.9 15.3 - - + -
202B ILE 2.8 15.3 + - - +
203B ALA* 3.7 2.1 - - - -
204B SER 2.9 25.7 + - - +
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Residues in contact with THR 174 (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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132B ILE 2.9 7.9 + - - +
133B ASP* 3.2 17.6 + - - +
134B ALA* 3.0 25.6 + - - +
172B LEU* 3.5 10.1 + - - +
173B LEU* 1.3 73.0 - - - +
175B SER* 1.3 66.6 + - - +
176B ILE 3.4 0.2 + - - -
179B ASP* 3.6 32.3 - - + +
189B LEU* 4.0 5.6 - - - +
204B SER* 3.1 31.4 + - - +
401B GOL 3.2 18.0 + - - +
501B GOL 4.2 4.3 - - - +
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Residues in contact with SER 175 (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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134B ALA 3.5 5.3 + - - -
173B LEU 4.2 0.4 + - - -
174B THR* 1.3 72.1 - - - +
176B ILE* 1.3 61.3 + - - +
177B ASP* 3.2 14.6 + - - +
178B ARG* 2.9 32.9 + - - +
179B ASP* 2.9 24.9 + - - +
186B ASP* 3.9 25.2 + - - +
189B LEU* 3.9 11.5 - - - +
204B SER 3.3 7.9 + - - -
205B GLY* 4.6 2.9 - - - -
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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