Contacts of the strand formed by residues 168 - 172 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ALA* 3.3 39.7 - - + +
52L ALA* 3.8 7.0 - - - -
53L PHE* 3.5 27.5 - - + -
56L TRP* 4.5 2.7 - - - -
140L GLY 3.2 9.2 + - - +
141L VAL* 3.5 2.9 - - + -
142L VAL* 2.9 27.0 + - - +
167L ASN* 1.3 79.4 - - - +
169L PHE* 1.3 61.4 + - - +
197L VAL* 3.3 29.8 - - - +
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Residues in contact with PHE 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L VAL* 3.3 21.8 - - + -
143L ALA 4.8 0.2 - - - -
144L GLY* 3.5 33.0 - - - -
158L MET* 3.6 22.0 - - + -
159L PHE* 3.6 30.3 - - + -
162L ALA* 3.6 26.7 - - + -
163L ILE* 4.1 9.2 - - + -
168L CYS* 1.3 74.4 - - - +
170L VAL* 1.3 76.3 + - - +
171L LEU* 3.5 30.5 - - + -
197L VAL 2.7 10.6 + - - +
198L MET* 3.9 15.5 - - - -
199L ASN* 3.0 33.0 + - - -
471L TYR* 4.6 2.2 - - - -
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Residues in contact with VAL 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L VAL* 5.3 0.2 - - + -
45L ALA* 4.0 43.1 - - + +
46L ILE* 4.3 5.6 - - + +
49L ALA* 4.1 11.2 - - + -
141L VAL* 4.1 11.2 - - + -
142L VAL 2.9 9.6 + - - +
143L ALA* 3.5 5.0 - - - +
144L GLY 3.1 21.0 + - - +
169L PHE* 1.3 82.5 - - - +
171L LEU* 1.3 61.6 + - - +
199L ASN* 3.6 9.6 - - + +
201L VAL* 4.0 18.4 - - + -
211L LEU* 3.8 26.4 - - + +
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Residues in contact with LEU 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L GLY* 3.4 11.4 - - - +
146L THR* 3.6 34.1 - - + +
155L PRO* 4.1 16.8 - - + -
158L MET* 5.0 0.4 - - - -
159L PHE* 4.4 3.6 - - + -
169L PHE* 3.5 18.3 - - + -
170L VAL* 1.3 73.3 - - - +
172L LYS* 1.3 63.4 + - - +
173L PRO* 3.7 9.3 - - + +
181L THR* 3.7 29.8 - - + +
185L ALA* 5.8 0.7 - - + -
198L MET* 3.9 18.6 - - + -
199L ASN 3.0 14.4 + - - +
200L VAL* 3.4 8.6 - - + -
201L VAL* 2.8 31.9 + - - +
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Residues in contact with LYS 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144L GLY 2.7 13.6 + - - +
145L ILE* 3.2 7.9 - - + -
146L THR 3.2 18.4 + - - -
171L LEU* 1.3 73.3 - - - +
173L PRO* 1.3 86.3 + - - +
175L GLU* 3.2 1.6 + - - -
201L VAL* 3.1 18.4 - - + +
203L GLY 3.1 32.0 + - - +
204L ASP* 4.4 0.6 - - - +
207L ALA* 4.0 20.6 - - + -
208L VAL* 3.5 25.2 - - + +
211L LEU* 3.9 18.8 - - + -
501L NAD 2.2 48.5 + - - +
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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