Contacts of the strand formed by residues 188 - 194 (chain A) in PDB entry 1Z6Z
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU* 4.1 23.6 - - + -
147A ARG* 3.5 47.3 - - - +
149A VAL* 4.1 12.1 - - + -
181A LEU* 4.9 0.7 - - + -
185A GLU* 2.8 38.6 + - + +
186A PRO* 3.9 6.1 - - - +
187A ASN* 1.3 79.3 - - - +
189A ARG* 1.3 70.7 + - - +
190A VAL* 3.5 16.1 + - + +
249A SER* 3.3 14.9 + - - -
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Residues in contact with ARG 189 (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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146A ASN* 4.1 17.9 - - - +
147A ARG 2.9 10.0 + - - +
148A THR* 3.2 19.1 - - - +
149A VAL 3.0 25.1 + - - -
186A PRO 5.7 2.7 - - - -
187A ASN 5.0 4.7 - - - +
188A VAL* 1.3 72.2 - - - +
190A VAL* 1.3 59.9 + - - +
245A ASP* 2.8 56.0 + - - +
246A GLU 4.0 0.4 - - - -
247A PHE* 2.9 48.0 + - + +
249A SER* 3.7 27.5 - - - +
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Residues in contact with VAL 190 (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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149A VAL* 3.6 16.6 - - + -
178A PHE* 3.4 50.3 - - + +
181A LEU* 4.0 13.5 - - + -
182A ALA* 3.9 22.4 - - + -
188A VAL* 3.9 11.9 - - + +
189A ARG* 1.3 75.0 - - - +
191A LEU* 1.3 65.6 + - - +
192A ASN* 5.2 0.2 - - - +
247A PHE* 3.3 13.5 - - - -
248A LYS 4.1 0.2 - - - +
249A SER* 3.1 10.7 + - - +
250A GLY* 2.8 31.3 + - - +
251A ALA 4.3 0.2 + - - -
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Residues in contact with LEU 191 (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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148A THR* 5.2 0.4 - - + -
149A VAL 3.0 11.9 + - - +
150A VAL* 3.4 9.2 - - + -
151A ASN* 2.8 27.4 + - - +
178A PHE* 4.1 0.7 - - - -
190A VAL* 1.3 78.1 - - - +
192A ASN* 1.3 72.8 + - - +
193A TYR* 3.8 6.5 + - + -
238A LEU* 3.7 29.4 - - + -
241A LEU* 4.7 9.4 - - + -
242A LEU* 4.1 16.6 - - + -
247A PHE* 3.7 32.1 - - + -
251A ALA 4.2 2.7 - - - +
253A VAL* 3.8 32.3 - - + -
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Residues in contact with ASN 192 (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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151A ASN* 2.8 33.6 + - - +
153A SER* 4.3 3.4 - - - -
175A ASP* 3.4 47.0 + - - +
178A PHE* 3.4 17.9 - - - +
179A GLN* 4.4 2.4 - - - +
191A LEU* 1.3 72.9 - - - +
193A TYR* 1.3 58.9 + - - +
194A ALA 4.1 0.2 + - - -
250A GLY* 3.2 25.3 + - - -
251A ALA 3.2 13.2 + - - +
252A HIS* 3.5 5.8 - - - +
253A VAL* 2.8 30.3 + - - +
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Residues in contact with TYR 193 (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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16A PHE* 4.3 3.6 - + - -
150A VAL* 4.4 4.3 - - + -
151A ASN 2.9 12.8 + - - +
152A ILE* 3.5 11.4 - - + -
153A SER* 2.6 28.3 + - - -
191A LEU* 3.8 8.9 - - + -
192A ASN* 1.3 72.7 - - - +
194A ALA* 1.3 60.9 + - - +
195A PRO* 3.4 31.6 - - + +
234A SER* 3.1 29.7 + - - -
237A LYS* 3.5 13.6 - - + +
238A LEU* 3.8 42.8 - - + -
241A LEU* 3.7 31.4 - - + -
253A VAL* 3.3 12.3 - - + -
254A ASP 4.4 1.1 - - - -
255A PHE* 3.6 20.0 - - - -
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Residues in contact with ALA 194 (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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153A SER* 4.0 2.7 - - - -
154A SER* 3.8 23.8 - - - +
155A LEU* 4.1 2.0 - - - +
192A ASN 4.1 0.6 + - - -
193A TYR* 1.3 73.0 - - - +
195A PRO* 1.3 61.9 - - + +
196A GLY 3.3 4.3 - - - +
252A HIS* 3.8 25.5 - - + +
253A VAL 2.9 11.5 + - - +
254A ASP* 3.3 14.2 - - - +
255A PHE 2.8 31.9 + - - -
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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