Contacts of the strand formed by residues 168 - 172 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ALA* 3.2 39.5 - - + +
52F ALA* 3.8 11.4 - - - -
53F PHE* 3.4 29.8 - - + -
56F TRP* 4.4 3.1 - - - -
140F GLY 3.1 7.7 + - - +
141F VAL* 3.3 5.6 - - - -
142F VAL* 2.8 33.3 + - - +
167F ASN* 1.3 78.3 - - - +
169F PHE* 1.3 55.6 + - - +
197F VAL* 3.2 21.5 - - - +
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Residues in contact with PHE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F VAL* 3.4 24.0 - - + -
143F ALA 4.6 0.2 - - - -
144F GLY* 3.7 20.4 - - - -
158F MET* 3.6 24.9 - - + -
159F PHE* 3.6 26.7 - + + -
162F ALA* 3.5 32.8 - - + -
163F ILE* 4.3 7.0 - - + -
168F CYS* 1.3 74.2 - - - +
170F VAL* 1.3 87.6 + - - +
171F LEU* 3.8 21.8 - - + -
197F VAL 2.7 12.0 + - - +
198F MET* 3.8 20.0 - - - -
199F ASN* 3.1 33.4 + - - -
221F SER* 5.8 0.2 - - - -
471F TYR* 4.6 1.6 - + - -
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Residues in contact with VAL 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F VAL* 5.1 0.4 - - + -
45F ALA* 3.9 42.6 - - + +
46F ILE* 4.3 6.5 - - + +
49F ALA* 4.1 1.8 - - + -
141F VAL* 4.0 20.4 - - + -
142F VAL 2.9 10.9 + - - +
143F ALA* 3.4 3.6 - - - +
144F GLY 3.0 22.7 + - - +
169F PHE* 1.3 82.7 - - - +
171F LEU* 1.3 61.4 - - - +
172F LYS 4.0 0.2 + - - -
199F ASN* 3.4 6.7 - - - +
201F VAL* 4.1 17.7 - - + -
211F LEU* 3.7 27.1 - - + +
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLY* 3.5 13.2 - - - +
146F THR* 3.7 30.3 - - + +
155F PRO* 4.0 18.4 - - + -
158F MET* 5.1 0.4 - - - -
159F PHE* 4.4 2.9 - - + -
169F PHE* 3.8 17.4 - - + -
170F VAL* 1.3 74.2 - - - +
172F LYS* 1.3 63.5 + - - +
173F PRO* 3.7 8.3 - - + +
181F THR* 3.8 27.6 - - + +
185F ALA* 5.6 0.4 - - + -
198F MET* 3.9 20.0 - - + -
199F ASN 2.7 16.4 + - - +
200F VAL* 3.5 10.1 - - + -
201F VAL* 2.7 34.0 + - - +
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Residues in contact with LYS 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLY 2.8 13.9 + - - +
145F ILE* 3.5 11.0 - - + +
146F THR 3.4 18.0 + - - -
171F LEU* 1.3 73.1 - - - +
173F PRO* 1.3 88.5 + - - +
174F SER* 4.5 1.2 - - - +
175F GLU* 3.1 26.1 + - - -
201F VAL* 3.2 16.2 - - + +
203F GLY 3.2 25.5 + - - +
204F ASP* 4.4 3.0 - - - +
207F ALA* 3.9 22.0 - - + -
208F VAL* 3.7 26.7 - - + +
211F LEU* 4.0 20.4 - - + -
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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