Contacts of the strand formed by residues 189 - 193 (chain H) in PDB entry 4XLQ
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 ARG 189 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155G ARG* 5.5 7.5 - - - +
29H GLU* 4.5 11.7 + - - -
185H ARG* 4.5 0.4 - - - -
186H LEU* 2.9 46.3 + - + +
188H GLN* 1.3 85.6 + - + +
190H THR* 1.3 55.2 + - - +
191H ASP* 3.3 36.7 + - - +
192H LEU* 3.3 25.5 - - + +
722J GLU* 4.9 3.1 - - - -
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Residues in contact with THR 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H ASP* 3.8 22.9 + - - +
184H THR 3.3 16.9 + - - +
185H ARG* 3.5 23.3 - - - +
188H GLN 3.8 2.3 + - - +
189H ARG* 1.3 71.4 - - - +
191H ASP* 1.3 61.7 + - - +
192H LEU 3.0 10.5 + - - -
720J LEU 5.5 3.1 + - - -
721J VAL* 5.5 7.8 - - + +
722J GLU* 3.4 41.9 + - + +
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Residues in contact with ASP 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ARG* 5.8 1.7 + - - -
29H GLU* 4.2 4.6 - - - +
30H ARG* 3.4 46.8 + - + +
183H ASP* 4.7 3.8 - - - -
189H ARG* 3.3 45.7 + - - +
190H THR* 1.3 80.4 + - - +
192H LEU* 1.3 60.5 + - - +
722J GLU* 4.1 16.6 - - - +
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Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PRO* 3.5 28.9 - - + -
28H LEU 3.0 10.8 - - - +
29H GLU* 5.0 0.2 - - - +
183H ASP* 3.2 25.5 - - - +
184H THR* 3.2 26.8 + - + +
185H ARG 4.1 2.7 - - - +
186H LEU* 3.5 32.1 - - + -
189H ARG* 3.3 49.1 - - - +
190H THR 3.0 2.0 + - - -
191H ASP* 1.3 78.0 - - - +
193H ASP* 1.3 70.2 + - - +
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Residues in contact with ASP 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU 3.4 7.3 - - - +
27H PRO* 3.3 8.1 - - - +
28H LEU* 2.5 47.0 + - + +
29H GLU 3.5 10.8 - - - -
30H ARG* 3.3 14.4 - - - -
31H GLY* 3.3 17.0 + - - -
33H GLY* 3.6 19.9 + - - +
34H VAL* 4.5 2.1 + - - +
181H VAL* 4.4 10.7 - - + +
182H GLU 3.2 8.5 - - - +
183H ASP* 3.9 9.0 - - - +
184H THR* 4.0 3.1 - - - -
192H LEU* 1.3 81.6 - - - +
194H LYS* 1.3 58.6 + - - +
195H LEU* 3.3 8.5 - - + +
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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