Contacts of the strand formed by residues 152 - 157 (chain B) in PDB entry 6UPR
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 VAL 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.4 38.1 - - + -
46B ASN 3.3 1.9 + - - +
47B ILE* 3.8 18.8 - - + -
48B LEU 2.8 30.7 + - - -
150B ILE* 3.2 9.6 - - - +
151B HIS* 1.3 76.2 - - - +
153B CYS* 1.3 57.8 + - - +
154B LEU* 4.1 4.9 - - + +
179B VAL* 5.1 0.9 - - - -
180B ASN 3.8 5.2 - - - +
182B ILE* 3.7 31.2 - - + -
279B MET* 4.0 11.9 - - + -
288B LEU* 3.7 21.3 - - + -
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Residues in contact with CYS 153 (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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48B LEU* 3.2 27.4 - - + -
50B VAL* 4.1 19.3 - - - -
152B VAL* 1.3 73.2 - - - +
154B LEU* 1.3 68.3 + - - +
155B TYR* 3.5 10.5 + - - -
175B LEU* 4.5 8.1 - - - -
179B VAL* 3.5 30.7 - - + +
180B ASN 3.0 9.3 + - - +
181B ILE* 3.5 6.9 - - - +
182B ILE 2.8 28.6 + - - -
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Residues in contact with LEU 154 (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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47B ILE* 4.5 11.4 - - + -
48B LEU 2.8 11.2 + - - +
49B CYS* 4.8 1.8 - - - -
50B VAL 3.1 24.3 + - - -
60B LEU* 4.8 0.4 - - + -
61B MET* 3.6 30.3 - - + -
64B LEU* 4.3 12.8 - - + -
152B VAL* 4.1 2.9 - - + -
153B CYS* 1.3 72.3 - - - +
155B TYR* 1.3 58.7 + - - +
156B PHE* 3.4 19.2 - - + -
182B ILE* 3.6 32.8 - - + +
184B ILE* 4.1 17.3 - - + -
276B LEU* 4.1 16.4 - - + -
279B MET* 4.1 21.1 - - + -
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Residues in contact with TYR 155 (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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50B VAL* 3.4 33.2 - - + -
51B GLY* 5.8 0.2 - - - -
107B PHE* 3.6 12.2 - + - -
153B CYS* 3.5 10.0 + - - -
154B LEU* 1.3 70.1 - - - +
156B PHE* 1.3 77.9 + - - +
157B ILE* 3.3 10.2 + - + +
167B LEU 3.5 7.4 + - - -
168B ASP* 3.1 52.0 + - + -
171B THR* 3.6 18.2 - - + -
172B MET* 3.7 28.0 - - + -
175B LEU* 4.8 4.0 - - + -
181B ILE* 4.2 19.3 - - + -
182B ILE 3.1 10.1 + - - +
183B PRO* 3.7 5.1 - - + +
184B ILE* 3.1 25.2 + - - +
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Residues in contact with PHE 156 (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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49B CYS* 4.0 17.7 - - + -
50B VAL 2.9 19.5 + - - +
51B GLY* 4.0 7.9 - - - -
52B GLU* 4.9 1.9 + - - +
55B ILE* 3.9 26.5 - - + -
56B GLY 4.2 2.9 - - - -
57B LYS* 3.7 38.6 - - + -
60B LEU* 3.5 31.0 - - + -
61B MET* 4.4 5.6 - - + -
154B LEU* 3.4 27.1 - - + -
155B TYR* 1.3 83.3 - - - +
157B ILE* 1.3 59.7 + - - +
158B THR* 4.0 3.5 + - - +
168B ASP* 4.9 1.9 - - - +
184B ILE* 3.5 20.6 - - + -
186B ALA* 4.0 21.1 - - + -
239B VAL* 5.4 0.4 - - + -
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Residues in contact with ILE 157 (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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155B TYR* 3.9 15.5 - - + +
156B PHE* 1.3 75.2 - - - +
158B THR* 1.3 74.9 + - - +
159B PRO 3.5 0.3 - - - -
163B SER 5.3 1.8 - - - +
164B LEU* 3.7 27.6 - - + -
168B ASP* 4.3 16.2 - - - +
172B MET* 5.0 4.5 - - + -
183B PRO* 4.2 20.9 - - + -
184B ILE 2.7 19.7 + - - +
185B ILE* 3.5 5.8 - - + +
186B ALA* 3.0 25.0 + - - +
199B PHE* 4.4 7.4 - - + -
203B ILE* 3.8 34.5 - - + -
207B LEU* 6.0 0.2 - - + -
236B PRO* 4.8 2.7 - - + -
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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