Contacts of the strand formed by residues 142 - 147 (chain K) in PDB entry 1HZH
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 142 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121K VAL* 4.5 8.5 - - + -
123K PRO* 4.0 13.2 - - - -
124K LEU* 3.3 12.8 - - - +
141K GLY* 1.3 76.4 - - - -
143K LEU* 1.3 62.0 + - - +
144K VAL* 4.3 2.9 - - + -
154K VAL* 6.4 0.9 - - + -
157K TRP* 3.5 13.1 - - + -
188K SER* 3.9 1.0 - - - -
189K SER* 3.0 31.3 + - - +
208K CYS* 2.0 56.3 - - + -
210K VAL* 5.3 2.5 - - + -
221K LYS 4.1 7.6 - - - -
225K ALA* 4.9 2.2 - - - -
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Residues in contact with LEU 143 (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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120K SER 3.0 5.7 - - - +
121K VAL* 3.3 3.1 - - - -
122K PHE* 2.9 51.4 + - + +
124K LEU* 4.4 12.3 - - + -
142K CYS* 1.3 77.6 - - - +
144K VAL* 1.3 60.8 + - - +
145K LYS* 4.4 13.7 - - + -
186K SER* 4.2 15.0 - - - +
187K LEU 3.7 16.2 - - - +
188K SER* 3.7 15.9 - - - -
124M GLN* 3.7 23.6 - - - +
131M SER* 4.2 18.8 - - - +
133M VAL* 4.7 15.3 - - + -
178M THR* 5.1 4.3 - - + +
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Residues in contact with VAL 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K PRO* 3.2 31.4 - - + -
120K SER 3.9 3.8 - - - -
121K VAL* 4.8 2.2 - - + +
142K CYS* 4.4 3.6 + - + -
143K LEU* 1.3 75.9 - - - +
145K LYS* 1.3 57.5 + - - +
147K TYR* 3.8 16.3 - - + -
152K VAL* 4.1 5.4 - - + -
154K VAL* 3.8 14.4 - - + -
186K SER* 3.6 2.1 + - - -
187K LEU* 3.0 47.2 + - + +
189K SER* 5.8 1.8 - - - +
210K VAL* 3.7 39.9 - - + -
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Residues in contact with LYS 145 (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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119K PRO* 3.6 2.3 - - - +
120K SER* 2.9 40.3 + - - +
122K PHE* 4.8 6.1 - - + -
143K LEU* 4.4 12.3 - - + -
144K VAL* 1.3 75.4 - - - +
146K ASP* 1.3 116.9 + - + +
147K TYR* 3.6 1.5 + - - -
179K GLN* 3.6 16.4 - - - +
185K TYR 4.0 0.2 - - - -
186K SER* 3.8 15.5 - - - +
124M GLN* 4.2 17.9 - - - +
129M THR* 4.3 19.5 + - - +
131M SER* 3.2 28.5 - - - +
180M THR* 4.7 12.4 - - - +
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Residues in contact with ASP 146 (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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117K LYS* 2.9 27.4 - - - -
118K GLY 3.0 6.8 - - - +
120K SER* 4.3 3.7 + - - +
145K LYS* 1.3 122.7 + - + +
147K TYR* 1.3 58.2 + - - +
179K GLN* 3.3 13.9 + - - +
182K SER* 4.0 7.1 + - - -
184K LEU* 3.3 30.0 - - + +
185K TYR 3.3 11.0 + - - -
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Residues in contact with TYR 147 (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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117K LYS* 4.0 7.0 - - - -
118K GLY 4.0 0.4 - - - -
119K PRO* 3.6 22.0 - - + -
144K VAL* 3.8 24.0 - - + -
146K ASP* 1.3 75.3 - - - +
148K PHE* 1.3 70.1 + - - +
149K PRO 4.2 1.3 - - - -
150K GLU* 3.5 26.2 + - + +
152K VAL* 3.2 31.9 + - + +
176K ALA* 3.4 24.1 - - - +
184K LEU* 3.6 5.4 - - - +
185K TYR* 3.0 64.2 + + + +
187K LEU* 3.6 25.8 - - + +
212K HIS* 3.9 10.3 - + + -
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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