Contacts of the strand formed by residues 141 - 145 (chain A) in PDB entry 1Z16
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 ILE 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.5 4.0 - - + -
138A PRO* 3.5 38.4 - - + +
139A GLN 5.6 0.2 - - - -
140A ARG* 1.3 75.6 - - - +
142A ALA* 1.3 76.1 + - - +
143A ILE* 4.1 13.5 - - + -
162A LEU* 4.1 21.5 - - + -
167A ALA* 4.0 26.0 - - + -
168A ASN 3.0 21.2 + - - +
169A VAL* 3.5 6.8 - - + +
170A VAL* 2.7 33.6 + - - +
171A PHE 3.7 0.2 + - - -
194A ILE* 4.3 1.1 - - - -
196A PHE* 3.4 19.3 - - + +
198A TYR* 5.2 0.9 - - + +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 1.3 77.7 - - - +
143A ILE* 1.3 64.6 + - - +
144A VAL* 4.2 2.7 - - + -
171A PHE* 3.4 42.4 - - + +
189A LEU* 4.1 1.3 - - + -
194A ILE* 3.9 17.9 - - + +
196A PHE 3.0 5.3 + - - +
197A VAL* 3.2 13.6 - - + +
198A TYR 3.1 22.9 + - - -
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 4.1 9.9 - - + -
142A ALA* 1.3 79.8 - - - +
144A VAL* 1.3 67.0 + - - +
155A ALA* 3.7 21.5 - - + +
158A VAL* 4.3 2.9 - - + -
159A GLN* 3.6 38.4 - - + +
162A LEU* 4.1 16.6 - - + -
169A VAL* 4.2 15.3 - - + -
171A PHE* 3.1 6.9 + - - +
172A PHE* 3.3 30.3 - - + -
173A ASP 3.0 24.1 + - - +
198A TYR* 3.4 20.6 - - + +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 4.8 2.5 - - + -
143A ILE* 1.3 86.5 - - - +
145A HIS* 1.3 67.3 + - - +
171A PHE* 4.5 11.0 - - + -
173A ASP* 3.1 11.9 - - + +
175A ILE* 4.1 24.7 - - + -
185A LEU* 4.1 31.0 - - + -
197A VAL* 4.2 17.7 - - + -
198A TYR 2.9 7.6 + - - +
199A TYR* 3.3 26.1 - - + -
200A GLY 2.8 23.4 + - - -
209A ILE* 5.6 0.4 - - + -
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 1.3 79.5 - - - +
146A ASP* 1.3 59.4 + - - +
147A LYS* 3.0 44.6 + - + -
151A GLY 3.8 6.7 - - - +
152A GLU* 3.5 20.9 - - + +
155A ALA* 3.7 13.2 - - + -
156A ARG* 5.5 0.6 + - - -
172A PHE* 3.4 38.0 - + - -
173A ASP 3.1 12.3 + - - -
174A GLY* 3.0 15.9 + - - -
175A ILE* 2.8 26.9 + - - +
199A TYR* 4.2 7.6 - - - -
200A GLY 3.2 13.9 - - - +
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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