Contacts of the strand formed by residues 199 - 204 (chain H) in PDB entry 1VPO
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H TRP* 3.4 8.9 - - - -
160H ASN* 2.8 39.1 + - - -
197H THR* 3.4 18.2 - - - +
198H VAL* 1.3 77.8 + - - +
200H CYS* 1.3 71.0 + - - +
201H ASN* 4.1 6.7 - - - +
212H ASP* 3.9 15.0 - - + -
213H LYS 3.3 24.9 - - - +
214H LYS* 3.4 11.3 - - + +
215H ILE* 4.8 0.4 - - - -
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Residues in contact with CYS 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H VAL* 4.0 16.6 - - - -
145H CYS* 2.0 50.5 - - + -
157H VAL* 4.4 4.9 - - + -
158H THR 3.2 7.9 - - - +
159H TRP* 3.4 22.7 - - + -
199H THR* 1.3 73.7 - - - +
201H ASN* 1.3 60.7 + - - +
202H VAL* 4.2 6.7 - - - -
211H VAL 3.8 0.9 - - - +
212H ASP* 3.3 1.9 - - - -
213H LYS* 2.9 36.5 + - - -
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Residues in contact with ASN 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H THR 3.4 1.0 - - - +
157H VAL* 3.1 6.4 - - - -
158H THR* 2.7 57.9 + - - +
160H ASN* 3.5 2.7 + - - +
161H SER* 2.7 41.4 + - - +
199H THR* 4.1 8.3 - - - +
200H CYS* 1.3 76.1 - - - +
202H VAL* 1.3 60.3 + - - +
210H LYS* 3.2 22.2 + - - +
211H VAL 3.5 4.3 - - - -
212H ASP* 2.7 25.9 + - - +
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Residues in contact with VAL 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H PRO* 4.4 8.5 - - + -
126H VAL* 3.8 36.8 - - + -
147H VAL* 3.8 29.4 - - + -
155H VAL* 3.6 25.4 - - + -
156H THR 3.2 2.5 - - - -
157H VAL* 4.2 9.4 - - + -
200H CYS* 4.2 11.2 - - - -
201H ASN* 1.3 79.6 - - - +
203H ALA* 1.3 62.9 + - - +
204H HIS 4.4 0.2 + - - -
209H THR* 4.1 1.7 - - - +
210H LYS* 3.4 3.8 - - - +
211H VAL* 2.7 39.4 + - + +
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Residues in contact with ALA 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H VAL* 3.1 8.6 - - - +
156H THR* 2.8 50.7 + - + +
202H VAL* 1.3 76.1 - - - +
204H HIS* 1.3 59.7 + - - +
205H PRO* 3.6 8.6 - - + +
209H THR 3.5 6.7 - - - +
210H LYS* 3.8 20.4 - - + +
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Residues in contact with HIS 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H THR* 4.0 0.2 - - + -
122H THR 3.4 13.4 + - - -
124H PRO* 3.6 27.9 - - + +
150H TYR* 3.9 2.3 - + + -
151H PHE 3.2 22.9 + - - -
152H PRO 2.9 23.1 + - - -
154H PRO 3.3 20.6 - - - -
155H VAL* 3.6 11.2 - - + -
203H ALA* 1.3 73.7 - - - +
205H PRO* 1.3 69.3 - - - +
206H ALA* 3.6 18.2 - - + +
207H SER* 2.5 30.2 + - - +
208H SER* 3.1 16.0 + - - -
209H THR* 2.9 17.3 + - - -
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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
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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