Contacts of the strand formed by residues 145 - 149 (chain L) in PDB entry 1DZH
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 ARG 145 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L MET* 4.8 0.6 - - - -
144L ASN* 1.3 78.2 + - - +
146L LEU* 1.3 76.2 + - - +
147L PHE* 3.5 32.4 - - + -
168L ALA* 4.1 3.5 - - - +
169L LYS* 3.5 55.1 - - - +
171L GLN* 2.9 31.8 + - - +
189L TRP* 3.5 38.4 - - + +
214L VAL 3.7 0.2 - - - +
216L VAL* 2.9 39.2 + - - +
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Residues in contact with LEU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L MET* 5.0 5.8 - - + -
145L ARG* 1.3 80.0 - - - +
147L PHE* 1.3 54.3 + - - +
148L GLY 3.9 0.9 - - - -
158L TYR* 3.7 19.5 - - + +
159L GLN* 5.2 1.8 - - - +
162L SER* 3.3 35.2 - - - +
168L ALA* 3.9 20.4 - - + +
169L LYS 2.8 11.1 + - - +
170L LEU* 4.1 17.5 - - + -
171L GLN 2.8 29.2 + - - -
213L LEU* 4.0 10.8 - - + -
214L VAL 3.7 3.4 - - - -
215L LEU* 3.5 40.6 - - + -
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Residues in contact with PHE 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ARG* 3.5 47.8 - - + -
146L LEU* 1.3 72.1 - - - +
148L GLY* 1.3 59.8 + - - +
171L GLN* 3.3 32.5 - - + -
173L LEU* 3.5 31.0 - - + -
175L PHE* 3.0 22.6 - - + -
185L ALA 4.8 1.6 - - - -
186L ILE* 3.8 36.3 - - + -
189L TRP* 3.7 32.3 - + + -
213L LEU* 3.7 1.1 - - - +
214L VAL 3.0 28.0 + - - +
216L VAL* 3.9 9.6 - - + -
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Residues in contact with GLY 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L PHE* 1.3 74.9 - - - +
149L ASP* 1.3 69.4 + - - +
154L PHE* 3.6 10.8 - - - -
170L LEU* 3.5 11.4 - - - +
171L GLN 3.1 8.5 + - - +
172L PRO* 3.4 3.6 - - - +
173L LEU 3.2 17.3 + - - -
175L PHE* 3.9 3.6 - - - -
212L VAL 3.5 9.0 - - - -
213L LEU* 3.5 12.7 - - - +
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Residues in contact with ASP 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L GLY* 1.3 74.6 - - - +
150L LYS* 1.3 70.2 + - - +
151L SER* 2.9 28.4 + - - -
152L LEU* 3.8 23.2 + - + +
154L PHE* 3.5 17.2 - - - -
172L PRO* 4.9 1.4 - - - +
173L LEU 3.2 4.3 - - - +
174L ASP* 3.6 2.8 - - - +
175L PHE* 2.7 39.1 + - + -
176L LYS* 3.2 26.0 + - - +
211L THR 4.1 6.3 - - - +
212L VAL* 2.8 18.2 + - - +
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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