Contacts of the strand formed by residues 184 - 189 (chain K) in PDB entry 2ZHX
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 CYS 184 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K LEU 4.6 0.9 - - - -
157K ALA* 3.5 42.2 - - - -
163K LEU* 3.4 26.0 - - + +
179K LEU* 3.8 30.9 - - + +
180K ALA 4.6 3.8 - - - +
181K ALA* 3.4 26.3 - - - +
182K GLY 3.5 2.2 - - - +
183K ASN* 1.3 87.4 - - - +
185K VAL* 1.3 64.0 + - - +
186K ALA* 4.3 0.3 + - - +
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Residues in contact with VAL 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 6.5 1.6 - - - -
112A ASN* 5.3 6.7 - - - +
163K LEU 3.1 6.5 + - - +
164K VAL* 3.3 8.8 - - + +
165K ALA* 3.0 24.0 + - - +
179K LEU* 4.9 0.6 - - - +
181K ALA* 5.6 0.2 - - - -
182K GLY 5.9 1.3 - - - +
183K ASN 5.0 0.7 - - - -
184K CYS* 1.3 78.5 - - - +
186K ALA* 1.3 69.1 + - - +
187K ILE* 5.5 0.9 - - + -
213K LEU* 4.1 34.1 - - + -
217K MET* 4.0 27.4 - - + -
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Residues in contact with ALA 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K ALA* 3.1 17.0 - - + +
167K LEU* 4.0 22.7 - - + -
176K LYS* 4.7 19.6 - - + +
179K LEU* 4.6 9.0 - - + -
184K CYS 4.3 1.0 + - - +
185K VAL* 1.3 81.1 - - - +
187K ILE* 1.3 62.9 - - - +
188K GLU* 4.1 5.4 + - + +
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Residues in contact with ILE 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K VAL* 5.0 1.1 - - + +
165K ALA 3.0 6.7 + - - +
166K ILE* 3.6 26.0 - - + -
167K LEU* 2.9 26.5 + - - +
168K TRP* 5.7 1.0 - - - +
185K VAL* 4.3 0.9 + - + -
186K ALA* 1.3 74.4 - - - +
188K GLU* 1.3 62.3 + - - +
206K PRO* 3.8 43.1 - - + +
209K ARG* 3.9 36.1 - - + +
210K ALA* 4.5 7.2 - - + +
213K LEU* 3.7 28.3 - - + -
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Residues in contact with GLU 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 3.3 16.1 - - - +
121A ARG* 5.9 1.2 + - - -
167K LEU* 3.5 20.9 - - + +
168K TRP* 5.6 0.4 - - - -
170K ARG* 5.5 0.2 + - - -
173K SER* 2.9 31.7 + - - +
176K LYS* 2.6 47.5 + - + +
186K ALA 4.1 4.2 + - - +
187K ILE* 1.3 78.5 - - - +
189K SER* 1.3 65.2 + - - +
209K ARG* 4.4 7.8 + - - +
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Residues in contact with SER 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 3.9 7.2 - - - +
167K LEU 3.3 6.1 + - - +
168K TRP* 3.3 18.7 + - - -
169K GLY* 2.9 20.8 + - - +
188K GLU* 1.3 78.9 - - - +
190K PRO* 1.3 88.4 + - - +
200K GLY 3.9 11.4 - - - -
201K PHE* 3.4 9.7 - - - -
204K SER* 4.1 11.4 + - - -
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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