Contacts of the strand formed by residues 168 - 172 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ALA* 3.3 40.2 - - + +
52I ALA* 3.8 6.5 - - - -
53I PHE* 3.4 29.1 - - + -
56I TRP* 4.4 3.8 - - - -
140I GLY 3.1 7.9 + - - +
141I VAL* 3.5 2.1 - - - -
142I VAL* 2.9 26.0 + - - +
167I ASN* 1.3 81.6 - - - +
169I PHE* 1.3 60.7 + - - +
197I VAL* 3.2 30.3 - - - +
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Residues in contact with PHE 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ALA* 4.9 0.2 - - - -
142I VAL* 3.4 23.3 - - + -
144I GLY* 3.6 33.7 - - - -
158I MET* 3.7 22.2 - - + -
159I PHE* 3.6 29.6 - - + -
162I ALA* 3.6 27.6 - - + -
163I ILE* 4.2 8.3 - - + -
168I CYS* 1.3 73.7 - - - +
170I VAL* 1.3 80.5 + - - +
171I LEU* 3.7 20.9 - - + -
197I VAL 2.7 11.3 + - - +
198I MET* 3.7 19.3 - - - -
199I ASN* 3.0 33.1 + - - -
221I SER* 5.8 0.2 - - - -
471I TYR* 4.7 1.6 - - - -
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Residues in contact with VAL 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I VAL* 5.2 0.7 - - + -
45I ALA* 4.1 35.2 - - + +
46I ILE* 4.3 6.5 - - + -
49I ALA* 4.2 2.5 - - + -
141I VAL* 4.1 22.2 - - + -
142I VAL 2.8 11.2 + - - +
143I ALA* 3.4 5.2 - - - +
144I GLY 3.0 21.7 + - - +
169I PHE* 1.3 81.9 - - - +
171I LEU* 1.3 60.4 + - - +
172I LYS 3.9 0.2 + - - -
199I ASN* 3.5 7.4 - - + +
201I VAL* 4.0 22.2 - - + -
211I LEU* 3.6 27.5 - - + +
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Residues in contact with LEU 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I GLY* 3.5 12.8 - - - +
146I THR* 3.6 32.3 - - + +
155I PRO* 4.0 16.4 - - + -
158I MET* 5.0 0.4 - - - -
159I PHE* 4.3 4.0 - - + -
169I PHE* 3.7 15.6 - - + -
170I VAL* 1.3 72.6 - - - +
172I LYS* 1.3 60.6 + - - +
173I PRO* 3.4 10.8 - - + +
181I THR* 3.7 29.4 - - + +
185I ALA* 5.7 0.4 - - + -
198I MET* 3.8 25.6 - - + -
199I ASN 2.8 16.0 + - - +
200I VAL* 3.5 9.6 - - + -
201I VAL* 2.8 31.1 + - - +
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Residues in contact with LYS 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I GLY 2.8 12.4 + - - +
145I ILE* 3.5 7.2 - - + -
146I THR 3.4 17.1 + - - -
170I VAL 3.9 0.4 + - - -
171I LEU* 1.3 72.5 - - - +
173I PRO* 1.4 90.4 + - - +
175I GLU* 3.4 0.6 + - - -
201I VAL* 3.3 14.8 - - + +
203I GLY 3.0 31.1 + - - +
204I ASP* 4.3 2.2 - - - +
207I ALA* 3.8 21.3 - - + -
208I VAL* 3.5 25.4 - - + -
211I LEU* 3.8 21.1 - - + -
501I NAD 2.9 40.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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