Contacts of the strand formed by residues 199 - 204 (chain A) in PDB entry 4ZXB
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 THR 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.3 9.2 - - - -
160A ASN* 2.7 43.4 + - - -
197A THR* 3.4 19.8 - - - +
198A VAL* 1.3 79.8 + - - +
200A CYS* 1.3 71.5 - - - +
201A ASN* 3.5 9.3 + - - +
212A ASP* 3.8 15.7 - - + -
213A LYS 3.5 22.4 - - - +
214A LYS* 3.8 7.8 - - + +
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Residues in contact with CYS 200 (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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126A VAL* 4.6 0.7 - - - +
145A CYS* 2.0 50.5 - - - -
157A VAL* 4.1 11.0 - - - -
158A THR 3.6 4.5 - - - -
159A TRP* 3.6 19.7 - - + -
199A THR* 1.3 74.0 - - - +
201A ASN* 1.3 60.2 + - - +
202A VAL* 3.6 18.5 + - - +
211A VAL 3.8 0.7 - - - +
212A ASP* 3.4 3.6 - - - -
213A LYS* 3.0 36.9 + - + +
215A ILE* 5.0 1.8 - - + -
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Residues in contact with ASN 201 (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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156A THR 3.4 2.3 - - - +
157A VAL* 3.4 4.3 - - - -
158A THR* 2.7 59.8 + - - +
160A ASN 3.3 8.7 - - - +
161A SER* 2.9 41.8 + - - +
199A THR* 3.5 9.2 + - - +
200A CYS* 1.3 73.2 - - - +
202A VAL* 1.3 59.9 + - - +
210A LYS* 4.7 14.7 - - - -
211A VAL 3.5 5.4 - - - -
212A ASP* 2.9 22.8 - - - +
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Residues in contact with VAL 202 (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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124A PRO* 4.4 8.1 - - + -
126A VAL* 3.8 30.7 - - + -
147A VAL* 3.7 26.9 - - + -
155A VAL* 3.4 24.9 - - + -
156A THR 3.4 1.8 - - - -
157A VAL* 4.2 7.4 - - + -
200A CYS* 3.6 24.0 - - - -
201A ASN* 1.3 77.2 - - - +
203A ALA* 1.3 62.5 + - - +
204A HIS 4.4 0.2 + - - -
209A THR* 4.1 1.0 + - - +
210A LYS* 3.3 3.7 - - - +
211A VAL* 2.8 40.7 + - + +
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Residues in contact with ALA 203 (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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155A VAL* 3.3 9.1 - - - +
156A THR* 2.9 44.9 + - - +
202A VAL* 1.3 76.1 - - - +
204A HIS* 1.3 60.6 + - - +
205A PRO* 3.6 9.3 - - + +
209A THR 3.4 7.2 - - - +
210A LYS* 3.8 30.5 - - + +
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Residues in contact with HIS 204 (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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121A THR* 4.5 0.4 - - + -
122A THR 3.4 12.5 + - - -
124A PRO* 3.6 27.4 - - + +
150A TYR* 3.8 3.5 - + + -
151A PHE 3.4 23.2 - - - -
152A PRO 2.8 25.1 + - - -
154A PRO 3.4 18.8 - - - -
155A VAL* 3.6 15.5 - - + -
203A ALA* 1.3 71.7 - - - +
205A PRO* 1.3 68.9 - - + +
206A ALA* 3.9 9.1 - - + +
207A SER* 2.7 46.2 + - - +
208A SER 3.0 9.2 + - - -
209A THR* 2.9 18.9 + - - +
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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