Contacts of the strand formed by residues 175 - 182 (chain B) in PDB entry 5U03
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 PHE 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TYR* 3.3 26.2 - - + +
5B LEU* 3.8 31.4 - - + -
145B ILE* 6.1 0.2 - - + -
163B PHE* 4.1 26.5 - + + -
166B PHE* 4.1 10.8 - + - -
167B GLN* 3.5 47.3 - - + +
170B VAL* 3.9 12.6 - - + -
171B LYS 4.1 3.4 - - - +
172B ARG* 2.9 17.1 + - - +
173B GLU 3.3 1.8 + - - -
174B ASN* 1.3 81.2 - - - +
176B CYS* 1.3 77.3 + - - +
177B ASN* 4.3 13.2 - - + -
209B LEU* 5.9 2.5 - - + -
212B ASP* 5.3 0.4 - - - -
269B ARG* 3.1 17.5 + - - -
270B LEU* 4.3 2.0 - - - +
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Residues in contact with CYS 176 (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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3B TYR 2.8 7.4 + - - +
4B ILE* 4.0 19.7 - - + -
5B LEU 2.8 27.9 + - - -
175B PHE* 1.3 82.0 - - - +
177B ASN* 1.3 63.0 + - - +
178B ILE* 3.6 27.4 - - - -
212B ASP* 3.4 19.3 - - - -
213B LEU* 5.3 1.1 - - - -
265B TYR* 5.3 0.2 - - - -
266B PHE* 3.6 20.6 - - + -
269B ARG* 4.8 7.0 - - + -
270B LEU* 4.1 11.7 - - + -
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Residues in contact with ASN 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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5B LEU* 4.0 4.9 - - - +
7B THR* 3.8 12.6 + - - +
167B GLN* 5.4 2.4 + - - +
175B PHE* 4.3 15.0 - - + -
176B CYS* 1.3 71.7 - - - +
178B ILE* 1.3 74.1 + - - +
179B HIS* 3.9 1.6 + - - +
204B LEU* 4.3 4.5 - - - +
209B LEU* 3.4 36.4 - - - +
210B SER 3.4 25.1 - - - +
211B PRO* 3.5 12.5 - - - +
212B ASP* 2.7 40.1 + - - +
213B LEU 3.3 6.6 + - - -
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Residues in contact with ILE 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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4B ILE* 3.5 26.9 - - + -
5B LEU 2.8 13.1 + - - +
6B VAL* 4.2 13.0 - - + -
7B THR* 2.8 30.9 + - - -
19B ILE* 5.2 6.7 - - + -
23B VAL* 6.6 0.2 - - + -
176B CYS* 3.6 22.9 - - - -
177B ASN* 1.3 77.5 - - - +
179B HIS* 1.3 63.3 + - - +
180B VAL* 4.5 7.4 - - + -
213B LEU* 3.7 22.7 - - + +
215B VAL* 3.9 25.6 - - + -
266B PHE* 4.0 15.5 - - + -
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Residues in contact with HIS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 3.0 20.8 + - - +
8B GLY* 3.6 25.9 - - - -
151B VAL* 3.7 13.2 - - + -
177B ASN* 3.9 0.4 + - - +
178B ILE* 1.3 75.0 - - - +
180B VAL* 1.3 63.4 + - - +
181B SER* 4.3 6.1 - - - -
200B SER* 2.9 33.9 + - - -
201B VAL* 3.8 25.2 - - + +
204B LEU* 3.6 14.4 - - + +
211B PRO* 3.5 23.8 - - + -
213B LEU 3.1 8.1 + - - +
214B VAL* 3.2 9.0 - - + +
215B VAL 2.7 30.9 + - - +
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Residues in contact with VAL 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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6B VAL* 4.2 11.2 - - + -
7B THR 2.8 19.6 + - - +
8B GLY* 3.0 20.8 - - - -
9B GLY 3.0 8.1 + - - +
14B ILE* 3.6 36.0 - - + +
15B GLY 5.0 1.6 - - - +
16B LYS* 4.0 23.3 - - + +
19B ILE* 4.8 7.0 - - + -
178B ILE* 4.5 2.9 - - + -
179B HIS* 1.3 77.6 + - - +
181B SER* 1.3 64.9 + - - +
215B VAL* 3.4 33.0 - - + +
217B ARG* 5.1 2.2 - - + +
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Residues in contact with SER 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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9B GLY 4.7 5.4 - - - +
10B VAL* 3.9 9.2 - - - +
14B ILE* 3.4 9.8 - - - +
179B HIS* 3.9 12.5 + - - -
180B VAL* 1.3 75.2 - - - +
182B LEU* 1.3 68.1 + - - +
197B THR* 2.7 44.5 + - - -
200B SER* 4.5 1.4 - - - -
214B VAL* 4.6 2.0 - - - -
215B VAL 2.8 12.8 + - - -
216B CYS* 4.5 2.5 - - - -
217B ARG* 2.9 28.6 + - - +
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Residues in contact with LEU 182 (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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184A PRO* 5.9 8.1 - - + -
10B VAL* 3.8 31.8 - - + +
11B ILE* 4.5 10.1 - - + -
14B ILE* 3.6 22.7 - - + -
181B SER* 1.3 83.6 + - - +
183B VAL* 1.4 74.5 + - - +
184B PRO* 3.2 34.1 - - + +
193B LYS 4.2 1.0 - - - +
196B PRO* 4.4 2.1 - - - +
197B THR* 2.9 19.5 + - - -
217B ARG* 3.6 18.8 - - + +
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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