Contacts of the helix formed by residues 123 - 132 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.8 18.8 - - + +
114A HIS* 3.5 47.6 - - + +
130A GLU* 4.4 5.4 - - - +
134A LEU* 3.8 13.7 - - + -
7X ASN* 3.7 11.4 - - - +
121X VAL* 3.3 17.5 - - + +
122X ASP* 1.3 84.8 - - - +
124X HIS* 1.3 58.1 + - - +
126X CYS* 3.4 8.2 + - + +
127X ASP* 3.0 28.8 + - - +
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Residues in contact with HIS 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 5.7 3.6 - - + -
134A LEU* 3.5 40.2 - - + +
135A GLU* 3.0 33.0 + - + +
138A VAL* 3.4 28.6 - - + +
7X ASN* 6.3 0.2 - - - +
68X TYR* 2.8 39.4 + + - -
71X LYS* 5.4 0.9 - - + -
72X ARG* 3.6 12.4 + - - +
122X ASP* 3.3 8.6 + - - +
123X PRO* 1.3 80.3 - - + +
125X LEU* 1.3 59.2 + - - +
127X ASP* 3.5 8.4 + - - +
128X PHE* 3.1 25.3 + - + +
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Residues in contact with LEU 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X TYR* 4.4 7.2 - - + -
12X CYS* 4.0 28.5 - - + -
16X VAL* 4.3 13.9 - - + -
65X PHE* 5.3 0.2 - - + -
68X TYR* 3.2 33.3 + - + +
72X ARG* 4.3 0.2 - - - +
113X LEU* 4.4 12.3 - - + -
117X ALA* 3.9 21.3 - - + -
122X ASP* 2.9 23.7 + - - +
124X HIS* 1.3 73.7 - - - +
126X CYS* 1.3 65.6 + - - +
128X PHE* 3.5 12.2 + - + +
129X LEU* 3.1 36.4 + - + +
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Residues in contact with CYS 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 5.7 3.1 - - - +
114X HIS* 3.6 22.4 - - + +
117X ALA* 3.6 19.3 - - - -
118X THR* 3.5 28.7 - - - -
122X ASP 3.4 14.3 + - - -
123X PRO* 3.5 13.0 - - + +
125X LEU* 1.3 81.5 - - - +
127X ASP* 1.3 56.7 + - - +
129X LEU* 3.4 3.5 + - - +
130X GLU* 3.1 37.5 + - - +
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Residues in contact with ASP 127 (chain X).
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* 5.6 1.2 - - - +
130A GLU* 3.7 47.7 + - + +
131A SER* 5.0 3.5 + - - -
134A LEU* 6.2 0.7 - - + -
135A GLU* 5.1 7.3 - - - +
127H ASP* 5.6 1.0 - - - +
123X PRO 3.0 17.0 + - - +
124X HIS* 3.8 9.3 - - + +
125X LEU 3.3 0.2 - - - -
126X CYS* 1.3 75.1 - - - +
128X PHE* 1.3 60.2 + - - +
130X GLU* 4.2 11.5 - - - +
131X SER* 2.9 48.9 + - - -
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Residues in contact with PHE 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 5.8 4.0 - - - -
64X LYS* 3.7 24.2 - - + -
65X PHE* 3.5 20.6 - + - -
68X TYR* 3.6 38.1 - + + -
71X LYS* 6.2 2.5 - - - -
124X HIS* 3.1 19.4 + - + +
125X LEU* 3.6 9.4 - - + +
127X ASP* 1.3 77.9 + - - +
129X LEU* 1.3 68.9 + - + +
131X SER* 4.7 2.7 - - - -
132X GLU* 3.0 52.6 + - + +
133X TYR* 3.5 30.6 - + - -
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Residues in contact with LEU 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X PHE* 4.0 24.9 - - + -
110X LEU* 4.2 17.5 - - + +
113X LEU* 3.9 18.6 - - + +
114X HIS* 3.8 40.6 - - + +
117X ALA* 5.1 0.2 - - + -
125X LEU* 3.1 27.3 + - + +
126X CYS* 3.6 5.4 - - - +
128X PHE* 1.3 96.8 - - + +
130X GLU* 1.3 58.5 + - - +
133X TYR* 3.0 15.9 + - + +
134X LEU* 2.9 32.3 + - + +
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Residues in contact with GLU 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 4.0 12.3 - - - +
123H PRO* 4.3 7.8 - - - +
126H CYS* 5.7 2.5 - - - +
127H ASP* 3.6 44.6 - - + +
130H GLU* 3.9 17.8 - - - +
114X HIS* 2.9 28.2 + - - +
126X CYS* 3.1 24.5 + - - +
127X ASP* 3.2 9.2 + - - +
129X LEU* 1.3 77.5 - - - +
131X SER* 1.3 61.5 + - - +
134X LEU* 3.9 18.4 - - + +
135X GLU* 4.1 18.5 + - - +
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Residues in contact with SER 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ASP* 5.2 4.7 + - - -
127X ASP* 2.9 36.5 + - - -
128X PHE* 4.2 2.5 - - - -
130X GLU* 1.3 79.5 - - - +
132X GLU* 1.3 74.2 + - - +
135X GLU* 5.8 3.0 - - - +
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Residues in contact with GLU 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X HIS* 4.6 4.2 + - - -
64X LYS* 2.9 41.1 + - + +
128X PHE* 3.0 39.5 + - + +
131X SER* 1.3 90.2 - - - +
133X TYR* 1.3 79.8 + - + +
136X GLU* 4.2 12.0 - - - +
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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