Contacts of the helix formed by residues 123 - 132 (chain H) in PDB entry 1MFR
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 PRO 123 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H ASN* 3.7 11.2 - - - +
121H VAL* 3.3 17.3 - - + +
122H ASP* 1.3 83.5 - - - +
124H HIS* 1.3 57.8 + - + +
126H CYS* 3.4 9.1 + - + +
127H ASP* 3.0 28.8 + - - +
111X LEU* 3.7 18.8 - - + +
114X HIS* 3.5 44.0 - - + +
130X GLU* 4.3 5.9 - - - +
134X LEU* 3.7 17.7 - - + -
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Residues in contact with HIS 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H TYR* 2.8 40.9 + + - -
71H LYS* 5.4 0.4 - - + -
72H ARG* 3.6 13.1 + - - +
122H ASP* 3.3 8.2 - - - +
123H PRO* 1.3 79.2 - - + +
125H LEU* 1.3 59.2 + - - +
127H ASP* 3.5 8.7 + - + +
128H PHE* 3.1 24.4 + - + +
111X LEU* 5.7 3.1 - - + -
134X LEU* 3.4 39.8 - - + +
135X GLU* 3.0 32.8 + - + +
138X VAL* 3.3 29.1 - - + +
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Residues in contact with LEU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H TYR* 4.4 6.5 - - + -
12H CYS* 4.0 28.7 - - + -
16H VAL* 4.3 14.1 - - + -
65H PHE* 5.3 0.2 - - + -
68H TYR* 3.2 33.1 + - + +
113H LEU* 4.4 13.2 - - + -
117H ALA* 3.9 19.7 - - + -
122H ASP* 2.9 23.6 + - - +
124H HIS* 1.3 74.4 - - - +
126H CYS* 1.3 65.4 + - - +
128H PHE* 3.7 12.3 - - + -
129H LEU* 3.1 36.1 + - + +
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Residues in contact with CYS 126 (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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114H HIS* 3.6 21.5 - - + +
117H ALA* 3.6 18.4 - - - -
118H THR* 3.5 29.6 - - - -
122H ASP 3.4 14.3 + - - +
123H PRO* 3.5 12.6 - - + +
124H HIS 3.2 0.2 - - - -
125H LEU* 1.3 80.7 - - - +
127H ASP* 1.3 55.7 + - - +
129H LEU* 3.4 4.0 + - - +
130H GLU* 3.1 37.1 + - - +
130X GLU* 5.7 2.9 - - - +
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Residues in contact with ASP 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP* 5.6 0.5 - - - +
123H PRO 3.0 16.8 + - - +
124H HIS* 3.8 9.0 - - + +
125H LEU 3.3 0.2 - - - -
126H CYS* 1.3 74.7 - - - +
128H PHE* 1.3 61.0 + - - +
130H GLU* 4.2 11.7 - - - +
131H SER* 2.9 49.4 + - - -
127X ASP* 5.6 1.2 - - - +
130X GLU* 3.6 47.2 + - + +
131X SER* 4.9 4.0 + - - -
134X LEU* 6.4 0.4 - - + -
135X GLU* 5.0 7.8 - - - +
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Residues in contact with PHE 128 (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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64H LYS* 3.7 24.9 - - + -
65H PHE* 3.5 20.4 - + - -
68H TYR* 3.6 38.8 - + + -
71H LYS* 6.2 2.7 - - - -
124H HIS* 3.1 20.1 + - + +
125H LEU* 3.6 9.9 - - + +
126H CYS 3.3 0.2 - - - -
127H ASP* 1.3 78.6 - - - +
129H LEU* 1.3 68.3 + - + +
131H SER* 4.7 2.7 - - - -
132H GLU* 3.0 52.8 + - + +
133H TYR* 3.5 29.9 - + - -
135X GLU* 5.7 3.8 - - - -
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Residues in contact with LEU 129 (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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65H PHE* 4.0 33.4 - - + -
110H LEU* 4.3 16.4 - - + +
113H LEU* 3.9 19.3 - - + +
114H HIS* 3.8 40.6 - - + +
117H ALA* 5.1 0.2 - - + -
125H LEU* 3.1 26.7 + - + +
126H CYS* 3.6 4.7 - - - +
127H ASP 3.2 0.2 - - - -
128H PHE* 1.3 89.2 - - + +
130H GLU* 1.3 58.2 + - - +
133H TYR* 3.0 15.2 + - + +
134H LEU* 2.9 33.9 + - + +
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Residues in contact with GLU 130 (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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123A PRO* 4.4 7.1 - - - +
126A CYS* 5.7 2.1 - - - +
127A ASP* 3.7 44.5 - - + +
130A GLU* 3.9 9.8 - - - +
114H HIS* 2.9 29.3 + - - +
126H CYS* 3.1 23.9 + - - +
127H ASP* 3.7 9.0 - - - +
129H LEU* 1.3 77.8 - - - +
131H SER* 1.3 61.7 + - - +
134H LEU* 3.9 24.4 + - + +
135H GLU* 4.1 12.3 + - - +
130X GLU* 3.9 17.1 - - - +
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Residues in contact with SER 131 (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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127A ASP* 5.0 4.0 + - - -
127H ASP* 2.9 35.3 + - - -
128H PHE* 4.2 2.7 - - - -
130H GLU* 1.3 79.2 - - - +
132H GLU* 1.3 76.0 + - - +
133H TYR 3.6 0.2 - - - -
135H GLU* 5.8 2.8 - - - +
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Residues in contact with GLU 132 (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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61H HIS* 4.6 4.3 + - - -
64H LYS* 2.9 41.0 + - + +
128H PHE* 3.0 39.2 + - + +
131H SER* 1.3 90.6 - - - +
133H TYR* 1.3 79.8 + - + +
136H GLU* 4.2 11.7 - - - +
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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