Contacts of the strand formed by residues 146 - 151 (chain B) in PDB entry 1PV2
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 TYR 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B HIS* 4.2 1.3 - - - -
50B LYS* 3.1 22.7 - - + +
51B ILE 4.6 0.7 - - - -
52B LEU* 3.6 41.1 - - + +
93B GLU* 3.4 27.1 + - + -
131B LYS* 4.6 6.9 + - - +
136B VAL* 3.7 29.0 - - + +
140B LEU* 3.9 22.9 - - + -
144B SER* 2.8 13.6 + - - -
145B GLU* 1.3 78.7 - - - +
147B ALA* 1.3 60.7 + - - +
148B ALA 3.4 6.5 - - - +
173B TRP* 3.6 19.4 - + + -
179B ARG* 2.9 31.3 + - - +
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Residues in contact with ALA 147 (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 HIS* 3.4 17.7 - - + -
50B LYS 2.6 14.4 + - - +
90B PHE* 3.7 10.1 - - + -
146B TYR* 1.3 73.6 - - - +
148B ALA* 1.3 61.3 + - - +
179B ARG* 3.7 7.0 - - - +
180B PHE* 3.4 26.5 + - - +
277B MET* 3.6 19.5 - - + +
281B TYR* 3.3 24.0 - - + +
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Residues in contact with ALA 148 (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 LYS 3.9 2.0 + - - +
51B ILE* 4.2 11.7 - - + -
52B LEU* 2.9 29.5 + - - +
146B TYR* 3.4 3.8 - - - +
147B ALA* 1.3 83.8 + - - +
149B ILE* 1.3 65.9 + - - +
150B PHE 4.0 0.4 - - - -
173B TRP* 5.8 0.2 - - - -
179B ARG* 4.2 2.6 - - - +
180B PHE* 3.1 23.3 - - + +
182B ILE* 4.0 22.9 - - + -
277B MET* 4.1 9.2 - - + -
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Residues in contact with ILE 149 (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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52B LEU* 3.4 35.4 - - + +
54B ILE* 3.7 29.8 - - + -
140B LEU* 6.2 0.4 - - + -
146B TYR* 5.3 0.4 - - + -
148B ALA* 1.3 76.3 - - - +
150B PHE* 1.3 56.3 + - - +
151B VAL* 4.1 7.1 + - + -
170B ALA* 4.5 11.7 - - + +
171B LEU* 4.3 15.5 - - + -
173B TRP* 4.3 19.3 - - + -
174B ALA* 3.6 26.7 - - + -
179B ARG* 6.0 0.2 - - + -
180B PHE 2.9 9.8 + - - +
181B VAL* 3.4 10.7 - - + +
182B ILE* 2.7 33.4 + - - +
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Residues in contact with PHE 150 (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 ILE* 4.0 15.0 - - + -
52B LEU 2.7 14.5 + - - +
53B VAL* 3.5 7.7 - - + -
54B ILE* 2.8 32.1 + - - +
77B GLU 3.6 20.6 - - - -
78B THR* 3.7 22.0 - - - -
81B PRO* 3.9 15.5 - - + -
82B LEU* 3.8 23.3 - - + -
85B LEU* 6.1 0.9 - - + -
148B ALA 4.0 0.2 - - - -
149B ILE* 1.3 73.4 - - - +
151B VAL* 1.3 63.6 + - - +
152B PRO* 3.5 30.3 - - + +
182B ILE* 3.2 43.5 - - + -
184B LEU* 4.0 17.5 - - + -
269B LEU* 4.9 0.7 - - + -
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Residues in contact with VAL 151 (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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54B ILE* 4.0 17.3 - - + +
149B ILE* 4.3 14.1 - - + +
150B PHE* 1.3 77.2 - - - +
152B PRO* 1.3 69.1 - - + +
157B ALA* 5.0 0.2 - - + -
161B LEU* 3.7 17.0 - - + -
167B VAL* 6.1 0.4 - - + -
171B LEU* 5.1 4.5 - - + -
181B VAL* 5.8 0.9 - - + -
182B ILE 2.9 11.0 + - - +
183B SER* 2.5 39.4 + - - +
184B LEU 3.8 0.2 + - - -
187B GLY* 3.4 28.0 - - - +
190B ALA* 3.7 20.2 - - + -
191B PHE* 4.9 10.8 - - + -
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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