Contacts of the helix formed by residues 107 - 117 (chain C) in PDB entry 1UMD
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C GLY 3.4 8.5 - - - +
106C ILE* 1.3 90.9 - - + +
108C LEU* 1.3 65.1 + - - +
109C LYS* 4.1 14.8 - - + +
110C GLU* 3.0 40.8 + - + +
111C LEU* 3.1 11.0 + - - +
134C SER* 6.1 0.2 - - - +
137C LEU* 4.9 3.6 - - + -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.8 18.4 - - + -
102C LEU* 3.7 30.3 - - + +
106C ILE 3.5 1.8 + - - -
107C PRO* 1.3 72.5 - - - +
109C LYS* 1.3 54.8 + - - +
111C LEU* 4.4 6.3 - - + -
112C LEU* 2.8 45.6 + - + +
322C ILE* 6.5 0.2 - - + -
325C GLU* 3.5 42.6 - - + +
326C LEU* 3.8 28.5 - - + +
329C GLY* 4.1 12.6 - - - -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PRO* 4.5 11.2 - - + +
108C LEU* 1.3 79.7 - - - +
110C GLU* 1.3 59.7 + - + +
113C GLY* 2.8 27.4 + - - -
120C ALA* 3.6 25.1 - - + +
329C GLY* 4.0 12.8 - - - -
332C GLU* 3.6 52.5 + - + +
333C ALA* 3.8 1.7 - - - +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ILE* 3.9 17.3 - - + +
107C PRO* 3.0 32.9 + - + +
109C LYS* 1.3 81.3 - - + +
111C LEU* 1.3 64.9 + - - +
113C GLY* 3.8 0.2 - - - -
114C GLN* 3.0 24.4 + - - +
120C ALA 3.8 11.4 - - - +
122C PRO* 3.7 38.0 - - + +
132C PRO* 5.8 0.6 - - - +
133C GLY 4.9 0.3 - - - +
134C SER* 4.4 12.6 + - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 4.3 10.1 - - + -
55C TYR* 4.2 12.3 + - - +
98C HIS* 4.2 8.7 - - + +
101C ALA* 3.8 17.0 - - + -
102C LEU* 4.0 34.5 - - + +
106C ILE* 3.8 27.1 - - + +
107C PRO 3.1 13.0 + - - +
108C LEU* 3.8 10.3 - - + +
110C GLU* 1.3 76.2 - - - +
112C LEU* 1.3 62.8 + - + +
114C GLN* 3.3 7.6 + - - +
115C MET* 3.1 27.0 + - - +
132C PRO* 3.7 28.7 - - + -
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.6 5.6 - - + -
54C ARG* 5.1 7.2 - - + -
55C TYR* 3.9 26.7 - - + -
58C LEU* 3.9 20.2 - - + -
108C LEU* 2.8 33.6 + - + +
111C LEU* 1.3 70.1 - - + +
113C GLY* 1.3 67.3 + - - +
115C MET* 3.2 2.8 + - + -
116C LEU* 2.9 30.1 + - + +
326C LEU* 4.2 9.0 - - + +
329C GLY* 3.6 7.0 - - - -
330C LEU* 3.3 44.0 - - + +
333C ALA* 3.9 12.8 - - + -
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS 2.8 22.0 + - - -
110C GLU 3.8 1.8 - - - -
111C LEU 3.2 0.2 - - - -
112C LEU* 1.3 78.0 - - - +
114C GLN* 1.3 51.3 + - - +
116C LEU* 3.4 0.8 + - - -
117C ALA* 2.8 29.5 + - - -
118C THR* 3.0 27.4 + - - -
120C ALA* 3.9 8.1 - - - -
121C ASP* 3.5 8.5 - - - +
333C ALA* 3.8 3.8 - - - +
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Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B TYR* 5.4 0.5 - - - -
110C GLU 3.0 14.4 + - - +
111C LEU* 3.6 4.9 - - - +
112C LEU 3.2 0.2 - - - -
113C GLY* 1.3 76.3 - - - +
115C MET* 1.3 67.2 + - - +
116C LEU 3.4 0.2 + - - -
117C ALA* 3.4 10.2 + - - +
121C ASP* 3.4 35.1 + - - +
123C ASN* 4.2 2.9 - - + +
125C GLY* 5.5 0.5 - - - -
127C GLN* 3.4 17.0 + - - +
128C MET 2.9 24.0 + - - -
129C PRO* 4.3 3.6 - - - +
130C GLU* 3.1 11.1 + - - -
131C HIS* 2.9 46.7 + - - +
132C PRO* 3.7 12.3 - - + +
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Residues in contact with MET 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B TYR* 4.9 2.3 + - - -
55C TYR* 3.5 54.1 - - + +
58C LEU* 4.8 3.6 - - + -
64C THR* 2.8 30.2 + - + +
66C PHE 3.3 26.7 - - - +
67C ILE* 3.7 9.0 - - + -
111C LEU 3.1 16.4 + - - +
112C LEU* 3.2 8.0 + - - +
114C GLN* 1.3 78.7 - - - +
116C LEU* 1.3 68.3 + - + +
129C PRO* 3.4 15.4 - - + +
130C GLU* 3.3 33.7 - - - +
132C PRO* 6.1 0.7 - - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B TYR* 5.4 0.4 - - - -
58C LEU* 4.1 19.5 - - + -
63C LYS* 3.5 34.2 - - + +
64C THR* 4.5 0.2 - - - -
112C LEU* 2.9 20.7 + - - +
113C GLY 4.2 0.2 - - - +
115C MET* 1.3 89.3 - - + +
117C ALA* 1.3 70.8 + - - +
118C THR* 3.7 20.4 - - + +
330C LEU* 3.8 15.5 - - + -
333C ALA* 4.7 4.7 - - + -
334C GLU* 3.7 33.2 - - + +
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B TYR* 3.7 33.9 - - + -
302B ALA* 4.4 9.0 - - + +
113C GLY 2.8 9.9 + - - -
114C GLN 3.4 9.3 + - - +
116C LEU* 1.3 82.5 - - - +
118C THR* 1.3 59.8 + - - +
125C GLY* 4.1 17.3 - - - -
338C PRO* 4.7 1.9 - - - +
339C VAL* 3.4 22.1 + - - +
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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