Contacts of the strand formed by residues 168 - 172 (chain A) in PDB entry 4ZZ7
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 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 3.3 41.1 - - + +
52A ALA* 3.8 4.5 - - - -
53A PHE* 3.4 27.3 - - + -
56A TRP* 4.6 2.7 - - - -
140A GLY 3.0 10.2 + - - +
141A VAL* 4.3 3.1 - - + -
142A VAL* 2.9 28.9 + - - +
167A ASN* 1.3 79.6 - - - +
169A PHE* 1.3 60.7 + - - +
197A VAL* 3.2 30.7 - - - +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 3.2 23.6 - - + -
144A GLY* 3.5 34.8 - - - -
158A MET* 3.7 21.3 - - + -
159A PHE* 3.6 33.7 - - + -
162A ALA* 3.7 24.0 - - + -
163A ILE* 4.3 6.3 - - + -
168A CYS* 1.3 75.3 - - - +
170A VAL* 1.3 79.3 + - - +
171A LEU* 3.7 26.0 - - + -
197A VAL 2.7 11.1 + - - +
198A MET* 3.8 15.3 - - - -
199A ASN* 2.9 33.1 + - - -
221A SER* 5.6 0.4 - - - -
471A TYR* 4.6 1.8 - - - -
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Residues in contact with VAL 170 (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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42A VAL* 5.1 0.7 - - + -
45A ALA* 4.1 33.2 - - + +
46A ILE* 4.1 10.1 - - + +
49A ALA* 4.2 0.4 - - + -
141A VAL* 4.0 21.1 - - + -
142A VAL 2.9 10.5 + - - +
143A ALA* 3.2 6.1 - - + +
144A GLY 2.9 24.3 + - - +
169A PHE* 1.3 80.4 - - - +
171A LEU* 1.3 62.8 + - - +
199A ASN* 3.6 9.4 - - + +
201A VAL* 4.0 22.7 - - + -
211A LEU* 3.7 26.5 - - + +
217A VAL* 6.3 0.2 - - + -
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Residues in contact with LEU 171 (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 GLY* 3.5 15.9 - - - +
146A THR* 3.7 27.4 - - + +
155A PRO* 4.0 15.0 - - + -
158A MET* 4.9 0.7 - - - -
159A PHE* 4.4 3.4 - - + -
169A PHE* 3.7 21.5 - - + -
170A VAL* 1.3 74.4 - - - +
172A LYS* 1.3 57.0 + - - +
173A PRO* 3.3 9.1 - - + +
181A THR* 3.7 31.6 - - + +
198A MET* 4.1 16.6 - - + -
199A ASN 2.8 17.0 + - - +
200A VAL* 3.4 10.6 - - + -
201A VAL* 2.7 33.6 + - - -
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Residues in contact with LYS 172 (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 GLY 2.9 13.9 + - - +
145A ILE* 3.5 7.1 - - + -
146A THR 3.3 19.6 + - - -
170A VAL 4.1 0.2 + - - -
171A LEU* 1.3 72.3 - - - +
173A PRO* 1.3 85.6 + - - +
175A GLU* 3.2 1.4 + - - -
201A VAL* 3.2 16.6 - - + +
203A GLY 3.1 30.9 + - - +
207A ALA* 4.0 20.4 - - + -
208A VAL* 3.6 23.3 - - + -
211A LEU* 3.9 20.4 - - + -
501A NAD 2.3 52.4 + - - +
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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