Contacts of the helix formed by residues 107 - 117 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY 3.2 8.0 - - - +
106A ILE* 1.3 92.6 - - + +
108A LEU* 1.3 65.4 + - - +
109A LYS* 4.2 17.9 - - + +
110A GLU* 2.9 41.8 + - + +
111A LEU* 3.1 10.0 + - - +
137A LEU* 5.0 3.1 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.8 27.8 - - + -
102A LEU* 3.4 31.4 - - + +
106A ILE 3.4 2.5 + - - -
107A PRO* 1.3 70.8 - - - +
109A LYS* 1.3 54.6 + - - +
111A LEU* 4.4 9.0 - - + -
112A LEU* 2.8 46.3 + - + +
325A GLU* 3.4 42.4 - - + +
326A LEU* 3.9 17.7 - - + +
329A GLY* 4.1 12.8 - - - -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 3.0 14.6 - - + -
108A LEU* 1.3 80.8 - - - +
110A GLU* 1.3 62.9 + - - +
113A GLY* 2.8 26.9 + - - -
120A ALA* 3.6 23.7 - - + +
329A GLY* 3.8 13.9 + - - -
332A GLU* 3.7 45.9 + - + +
333A ALA* 3.8 2.2 - - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.9 12.3 - - + +
107A PRO* 2.9 39.0 + - + +
109A LYS* 1.3 85.1 - - + +
111A LEU* 1.3 64.8 + - - +
113A GLY* 3.9 0.5 - - - -
114A GLN* 3.1 23.0 + - - +
120A ALA 3.8 11.0 - - - +
122A PRO* 3.7 38.8 - - + +
123A ASN* 5.7 0.2 + - - -
132A PRO* 5.7 0.7 - - - +
133A GLY 5.0 0.2 - - - +
134A SER* 4.4 12.3 + - - -
108B GLN* 5.6 0.2 - - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.4 10.3 - - + -
55A TYR* 4.2 11.4 + - - +
98A HIS* 4.2 8.5 - - + +
101A ALA* 3.7 19.3 - - + -
102A LEU* 4.0 35.4 - - + +
106A ILE* 3.7 31.6 - - + +
107A PRO 3.1 7.8 + - - +
108A LEU* 3.8 9.6 - - + +
110A GLU* 1.3 76.7 - - - +
112A LEU* 1.3 61.5 + - + +
114A GLN* 3.3 7.4 + - - +
115A MET* 3.1 30.2 + - - +
132A PRO* 3.7 29.3 - - + +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.5 7.9 - - + -
54A ARG* 5.9 5.2 - - + +
55A TYR* 3.8 20.4 - - + -
58A LEU* 3.8 29.2 - - + -
108A LEU* 2.8 32.7 + - + +
111A LEU* 1.3 71.0 - - + +
113A GLY* 1.3 60.2 + - - +
114A GLN 3.1 0.2 - - - -
115A MET* 3.1 3.6 + - + -
116A LEU* 2.8 35.6 + - + +
326A LEU* 4.2 8.5 - - + +
329A GLY* 3.6 5.8 - - - -
330A LEU* 3.3 43.7 - - + +
333A ALA* 3.8 13.9 - - + -
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS 2.8 21.1 + - - -
110A GLU 3.5 1.5 + - - -
111A LEU 3.3 0.2 - - - -
112A LEU* 1.3 77.4 - - - +
114A GLN* 1.3 53.3 + - - +
116A LEU 3.6 0.2 - - - -
117A ALA* 2.7 29.5 + - - -
118A THR* 3.0 27.9 + - - -
120A ALA* 3.8 8.3 - - - -
121A ASP* 3.5 8.4 - - - +
333A ALA* 3.7 4.4 - - - +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU 3.1 14.5 + - - +
111A LEU* 3.6 6.2 - - - +
113A GLY* 1.3 74.6 - - - +
115A MET* 1.3 67.7 + - - +
116A LEU 3.3 0.3 + - - -
117A ALA* 3.4 10.6 + - - +
121A ASP* 3.4 34.5 + - - +
123A ASN* 4.1 2.4 - - + +
125A GLY* 5.5 0.4 - - - -
127A GLN* 3.4 16.0 + - - +
128A MET 2.9 24.0 + - - -
129A PRO* 4.3 3.6 - - - +
130A GLU* 3.2 11.5 + - - -
131A HIS* 2.9 47.5 + - - +
132A PRO* 3.7 12.8 - - + +
301D TYR* 5.5 0.3 - - - -
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 3.4 54.1 - - + +
58A LEU* 4.9 2.7 - - + -
64A THR* 2.7 35.3 + - + +
65A SER 4.8 0.2 + - - -
66A PHE 3.3 25.8 - - - +
67A ILE* 3.8 7.4 - - + -
111A LEU 3.1 15.3 + - - +
112A LEU* 3.1 10.6 + - - +
114A GLN* 1.3 79.0 - - - +
116A LEU* 1.3 69.8 + - + +
117A ALA* 3.9 0.5 + - - +
129A PRO* 3.5 11.9 - - + +
130A GLU* 3.3 30.5 - - - +
132A PRO* 6.1 0.4 - - - -
301D TYR* 5.1 1.7 + - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.3 17.7 - - + -
63A LYS* 3.7 34.9 - - + +
64A THR* 4.5 0.7 - - - -
112A LEU* 2.8 20.1 + - - +
113A GLY 4.1 0.4 - - - +
115A MET* 1.3 88.2 - - + +
117A ALA* 1.3 70.8 + - - +
118A THR* 3.4 18.0 + - + +
330A LEU* 3.9 13.9 - - + -
333A ALA* 4.4 7.9 - - + -
334A GLU* 3.7 35.9 - - + +
301D TYR* 5.5 0.9 - - - -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 2.7 10.0 + - - -
114A GLN 3.4 8.1 + - - +
115A MET 3.5 0.2 - - - -
116A LEU* 1.3 81.8 - - - +
118A THR* 1.3 59.0 + - - +
125A GLY* 4.1 18.6 - - - -
127A GLN 5.4 0.2 - - - +
338A PRO* 4.8 1.6 - - - +
339A VAL* 3.5 22.3 + - - +
301D TYR* 3.8 33.7 - - + -
302D ALA* 4.6 7.7 - - + +
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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