Contacts of the strand formed by residues 202 - 207 (chain H) in PDB entry 4JZJ
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 ILE 202 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H TRP* 3.4 6.8 - - - -
162H ASN* 2.6 48.6 + - - +
200H THR* 3.8 23.6 - - + -
201H TYR* 1.3 80.0 - - - +
203H CYS* 1.3 64.9 + - - +
204H ASN* 3.4 22.0 + - - +
215H ASP* 3.9 9.6 - - + -
216H LYS 3.2 22.4 - - - +
217H LYS* 4.2 11.0 - - + +
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Residues in contact with CYS 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H VAL* 3.9 0.7 - - - -
147H CYS* 2.0 49.8 - - + -
159H VAL* 4.1 7.9 - - + -
160H SER 3.5 3.6 - - - -
161H TRP* 3.6 24.2 - - + -
202H ILE* 1.3 73.7 - - - +
204H ASN* 1.3 59.6 + - - +
205H VAL* 3.8 16.2 - - - -
214H VAL 3.6 1.4 - - - +
215H ASP* 3.4 3.1 - - - -
216H LYS* 2.9 45.6 + - - -
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Residues in contact with ASN 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H THR 3.5 2.1 - - - +
159H VAL* 3.4 4.5 - - - -
160H SER* 2.8 44.4 + - - +
162H ASN* 3.5 5.4 + - - +
163H SER* 2.6 42.6 + - - +
202H ILE* 3.4 23.2 - - - +
203H CYS* 1.3 70.7 - - - +
205H VAL* 1.3 61.2 + - - +
206H ASN* 3.8 1.4 + - - +
213H LYS* 3.5 19.2 + - - +
214H VAL 3.6 4.9 - - - -
215H ASP* 2.7 21.4 + - - -
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Residues in contact with VAL 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PRO* 4.5 11.2 - - + -
128H VAL* 3.7 43.3 - - + -
149H VAL* 3.8 33.0 - - + -
157H VAL* 4.8 4.7 - - + -
158H THR 3.5 7.6 - - - +
159H VAL* 4.3 8.1 - - + -
203H CYS* 3.8 14.6 - - - -
204H ASN* 1.3 72.3 - - - +
206H ASN* 1.3 66.1 + - - +
207H HIS 4.4 0.2 + - - -
212H THR* 4.4 1.4 - - + +
213H LYS* 3.6 3.1 - - - +
214H VAL* 2.8 42.3 + - + +
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Residues in contact with ASN 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H PRO 4.5 0.2 - - - +
157H VAL* 3.5 4.4 - - - -
158H THR* 3.1 42.5 + - - +
204H ASN 3.8 1.3 + - - +
205H VAL* 1.3 76.5 - - - +
207H HIS* 1.3 60.6 + - - +
208H LYS* 3.4 42.8 + - - +
212H THR 3.4 10.7 - - - +
213H LYS* 3.2 32.8 - - + +
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Residues in contact with HIS 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LYS 3.7 9.2 - - - -
126H PRO* 3.5 29.9 - - + +
152H TYR* 3.9 2.6 - + - -
153H PHE 3.4 22.8 + - - -
154H PRO 2.9 23.3 + - - -
156H PRO 3.1 25.6 - - - -
157H VAL* 3.8 13.7 - - + -
205H VAL 4.3 0.4 - - - -
206H ASN* 1.3 72.5 - - - +
208H LYS* 1.3 65.0 + - - +
209H PRO* 3.7 22.3 - - + +
210H SER* 2.8 33.2 + - - -
211H ASN 3.3 6.9 + - - -
212H THR* 3.0 18.7 + - - +
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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