Contacts of the strand formed by residues 210 - 215 (chain A) in PDB entry 5VEB
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLY* 3.8 7.4 - - - -
124A PRO* 3.7 31.0 - - + +
203A VAL* 3.9 1.6 - - + +
204A ASN* 3.2 6.7 - - - +
205A HIS 2.8 34.1 + - - -
208A SER* 2.7 28.4 + - - -
209A ASN* 1.4 72.6 - - - +
211A LYS* 1.3 60.6 + - - +
212A VAL* 3.7 24.0 - - + +
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Residues in contact with LYS 211 (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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203A VAL 3.5 5.4 - - - +
204A ASN* 3.7 29.2 - - + +
209A ASN 3.6 6.2 + - - +
210A THR* 1.3 71.6 - - - +
212A VAL* 1.4 63.2 + - - +
213A ASP* 4.4 5.5 + - - +
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Residues in contact with VAL 212 (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 5.1 3.4 - - - +
126A VAL* 3.8 39.3 - - + +
201A CYS 3.4 1.9 - - - +
203A VAL* 2.8 43.0 + - + +
210A THR* 3.7 23.6 - - + -
211A LYS* 1.4 76.4 - - - +
213A ASP* 1.3 67.7 + - - +
214A LYS* 4.2 15.5 - - + +
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Residues in contact with ASP 213 (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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161A SER* 5.4 1.0 + - - -
200A ILE* 3.7 13.4 - - + +
201A CYS 3.5 4.3 - - - -
202A ASN* 3.1 30.7 + - - +
203A VAL 5.2 0.3 - - - +
211A LYS* 4.4 5.7 + - - +
212A VAL* 1.3 80.2 + - - +
214A LYS* 1.4 60.9 + - - +
215A ARG* 3.8 2.3 + - - +
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Residues in contact with LYS 214 (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* 3.3 48.1 + - + +
128A PRO* 4.0 18.5 - - + +
145A CYS* 4.3 2.5 - - - -
200A ILE* 3.2 3.9 - - - -
201A CYS* 2.9 44.3 + - - -
212A VAL* 3.8 9.9 - - + +
213A ASP* 1.4 71.2 - - - +
215A ARG* 1.3 73.9 + - - +
216A VAL* 3.6 2.4 + - - +
124B GLU* 3.7 30.3 + - - +
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Residues in contact with ARG 215 (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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128A PRO* 4.5 4.7 - - - +
194A LEU 6.0 0.2 + - - -
197A GLN 4.6 4.0 + - - -
198A THR* 3.3 30.6 + - - +
199A TYR* 3.5 17.7 - - - +
200A ILE* 3.7 22.2 - - + +
213A ASP 3.8 3.8 + - - +
214A LYS* 1.3 85.4 - - - +
216A VAL* 1.3 85.1 + - - +
217A GLU* 3.2 43.9 + - - +
218A PRO* 5.5 0.8 - - - +
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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