Contacts of the strand formed by residues 168 - 173 (chain H) in PDB entry 5MGX
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 168 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H THR* 3.8 1.2 - - - -
107H LEU* 2.8 48.8 + - + -
108H VAL* 2.9 38.9 + - + +
166H GLY 3.8 2.3 + - - -
167H GLU* 1.4 69.1 - - - +
169H ALA* 1.3 58.5 + - - +
197H GLU* 5.7 3.4 - - + -
198H VAL 3.2 7.0 - - - +
199H THR* 3.1 34.6 + - - +
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Residues in contact with ALA 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H LYS* 4.0 21.3 - - + -
105H LYS 3.3 13.0 - - - +
107H LEU* 4.0 6.1 - - - +
163H MET* 3.8 15.4 - - + +
167H GLU* 3.9 18.2 - - - +
168H THR* 1.3 74.7 - - - +
170H MET* 1.3 60.3 + - - +
171H VAL* 4.1 3.1 - - + -
196H LEU 3.6 0.9 - - - +
197H GLU* 3.6 2.9 - - - -
198H VAL* 2.8 33.9 + - - +
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Residues in contact with MET 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H TRP* 3.6 36.0 - - + -
104H LYS* 3.4 3.1 - - - -
105H LYS* 2.8 36.9 + - + +
107H LEU* 3.4 30.4 - - + +
169H ALA* 1.3 72.1 - - - +
171H VAL* 1.3 62.0 + - - +
172H THR* 4.3 0.4 - - - -
195H CYS* 3.8 27.8 - - - -
196H LEU 3.5 4.5 - - - +
197H GLU* 4.7 8.5 - - + +
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Residues in contact with VAL 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ILE* 5.3 0.2 - - + -
102H LEU* 3.8 29.8 - - + -
103H ARG 3.2 6.7 - - - +
104H LYS* 4.0 19.1 - - + -
155H ALA 5.0 0.2 - - - +
159H SER* 3.8 29.2 - - - +
163H MET* 5.7 2.5 - - - -
169H ALA* 4.9 3.8 - - + -
170H MET* 1.3 80.1 - - - +
172H THR* 1.3 65.8 + - - +
173H ALA* 3.9 4.4 + - + -
194H LEU 3.6 1.2 - - - +
195H CYS* 3.4 3.1 - - - -
196H LEU* 2.8 57.3 + - + +
198H VAL* 4.8 9.2 - - + -
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Residues in contact with THR 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H TRP* 3.7 24.9 - - + -
100H GLY 5.4 0.5 + - - -
101H LEU 3.6 2.1 - - - +
102H LEU* 3.3 4.9 + - - -
103H ARG* 2.8 54.8 + - - +
170H MET* 4.9 0.4 - - + -
171H VAL* 1.3 75.3 - - - +
173H ALA* 1.3 59.9 + - - +
194H LEU 3.5 5.2 - - - -
195H CYS* 4.5 17.7 - - + -
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Residues in contact with ALA 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H LEU 3.3 4.3 - - - -
102H LEU* 3.7 21.8 - - + -
155H ALA* 3.9 10.1 - - + -
171H VAL* 3.9 3.8 + - + -
172H THR* 1.3 74.4 - - - +
174H ASP* 1.3 62.2 + - - +
177H TYR* 4.7 2.0 - - + -
178H CYS* 3.6 21.8 - - - -
193H ALA* 3.4 5.2 - - - +
194H LEU 2.8 38.9 + - - +
196H LEU* 5.0 3.4 - - + -
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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