Contacts of the helix formed by residues 73 - 84 (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 HIS 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ALA 2.8 19.6 + - - +
71C ALA 4.4 1.3 - - - -
72C GLY* 1.3 79.1 - - - +
74C GLU* 1.3 61.5 + - - +
75C ALA 3.4 2.5 - - - -
76C ALA* 3.2 5.3 + - + +
77C GLN* 3.0 41.4 + - - +
94C TYR* 3.8 8.5 - - - -
96C ARG* 3.7 21.7 - - - -
202C GLU* 2.9 31.4 + - + +
204C ASN* 3.2 32.2 + - - +
267C VAL* 3.7 25.4 - - + +
268C TYR 3.8 15.0 + - - -
269C ARG* 4.3 4.2 - - - -
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Residues in contact with GLU 74 (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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45C MET* 3.6 38.6 - - + +
48C ALA* 3.7 18.2 - - + +
49C ARG* 2.7 46.5 + - + +
52C ASP* 4.9 0.9 - - - +
70C ALA* 3.8 3.6 - - - +
71C ALA* 3.3 13.4 + - - -
72C GLY* 2.7 27.1 + - - -
73C HIS* 1.3 76.7 + - - +
75C ALA* 1.3 57.7 + - - +
77C GLN* 4.6 4.3 - - - +
78C VAL* 2.9 36.9 + - - +
296C PRO* 4.2 5.0 - - + +
297C ILE* 4.8 2.0 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C MET* 3.6 11.9 - - - -
72C GLY 5.1 0.2 + - - -
73C HIS 3.4 0.6 - - - -
74C GLU* 1.3 77.6 - - - +
76C ALA* 1.3 62.8 + - - +
79C ALA* 3.0 28.3 + - - +
237C GLY 3.3 17.3 - - - +
238C MET 3.8 0.9 - - - -
240C VAL* 3.7 32.4 - - + +
243C SER* 4.6 1.1 - - - -
296C PRO* 3.5 26.9 - - + +
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Residues in contact with ALA 76 (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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73C HIS* 3.2 8.8 + - - +
75C ALA* 1.3 80.8 - - - +
77C GLN* 1.3 61.5 + - + +
79C ALA* 3.7 1.4 - - - +
80C ILE* 3.0 33.1 + - - +
202C GLU* 4.6 13.2 - - + -
237C GLY 3.5 5.3 + - - +
243C SER* 4.4 4.0 - - - -
265C LEU* 3.6 27.3 - - + +
267C VAL* 3.9 23.6 - - + -
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Residues in contact with GLN 77 (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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70C ALA* 4.1 4.4 - - - +
73C HIS* 3.0 32.7 + - - +
74C GLU* 4.2 3.3 - - - +
76C ALA* 1.3 75.7 - - - +
78C VAL* 1.3 63.5 + - + +
80C ILE* 3.4 5.6 + - + +
81C ALA* 3.2 18.5 + - - +
96C ARG 2.9 23.6 + - - +
97C ASP* 3.2 19.7 + - - +
99C GLY* 3.0 18.9 + - - -
100C LEU* 2.9 44.5 + - + +
202C GLU* 3.0 30.7 + - - +
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Residues in contact with VAL 78 (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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41C LEU* 3.7 21.8 - - + +
44C ASP* 3.6 26.0 - - + +
45C MET* 3.6 30.1 - - + +
48C ALA* 4.7 7.6 - - + -
74C GLU* 2.9 22.2 + - - +
75C ALA 4.3 1.1 - - - +
77C GLN* 1.3 73.7 - - + +
79C ALA* 1.3 66.3 + - - +
81C ALA* 3.3 1.4 + - - +
82C HIS* 3.1 46.9 + - + -
99C GLY 5.0 1.1 - - - +
103C ALA* 4.3 12.3 - - + -
240C VAL* 4.7 2.2 - - + -
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Residues in contact with ALA 79 (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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41C LEU* 5.1 1.3 - - - -
75C ALA 3.0 21.6 + - - +
76C ALA 3.7 2.5 - - - +
77C GLN 3.3 0.2 - - - -
78C VAL* 1.3 78.6 - - - +
80C ILE* 1.3 62.9 + - + +
82C HIS* 3.3 4.1 + - - -
83C ALA* 3.0 24.7 + - - +
240C VAL* 3.7 11.0 - - + +
243C SER* 3.5 13.5 - - - +
244C TYR* 3.4 39.4 - - - +
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Residues in contact with ILE 80 (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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76C ALA 3.0 22.2 + - - +
77C GLN* 3.7 8.1 - - - +
78C VAL 3.2 0.2 - - - -
79C ALA* 1.3 77.1 - - - +
81C ALA* 1.3 62.0 + - - +
83C ALA* 3.2 15.1 + - - +
84C ILE* 3.5 17.4 + - + +
100C LEU* 4.1 18.4 - - + -
170C VAL* 4.5 19.1 - - + -
172C THR* 3.6 26.0 - - + -
200C ILE* 3.9 36.3 - - + -
202C GLU* 4.7 7.4 - - + +
247C VAL* 4.5 8.3 - - + -
265C LEU* 4.1 11.9 - - + -
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Residues in contact with ALA 81 (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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77C GLN 3.2 4.7 + - - +
78C VAL 3.3 4.9 + - - +
80C ILE* 1.3 79.8 - - - +
82C HIS* 1.3 61.2 + - + +
84C ILE* 3.6 22.2 - - - +
86C PRO* 4.2 10.0 - - - +
100C LEU* 3.6 20.8 - - + +
103C ALA* 3.6 44.2 - - + +
104C LEU* 3.8 7.5 - - - +
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Residues in contact with HIS 82 (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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40C ARG* 3.9 22.2 + - + +
41C LEU* 3.6 29.3 - - + +
44C ASP* 2.5 29.8 + - - -
78C VAL* 3.1 32.3 + - + +
79C ALA 3.3 3.8 + - - +
80C ILE 3.1 0.6 - - - -
81C ALA* 1.3 81.3 - - + +
83C ALA* 1.3 61.2 + - - +
84C ILE 3.3 7.3 + - - +
103C ALA* 4.7 6.6 + - + -
244C TYR* 3.4 20.0 + - + -
248C LYS* 4.9 3.6 + - - -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA 3.0 15.3 + - - +
80C ILE 3.2 3.5 + - - +
82C HIS* 1.3 78.2 - - - +
84C ILE* 1.3 59.4 + - - +
244C TYR* 3.9 14.6 - - + +
247C VAL* 3.8 28.3 - - + -
248C LYS* 3.6 40.6 + - + +
251C VAL* 3.9 15.1 - - + +
255C ARG* 5.0 0.7 + - - -
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 3.6 19.5 - - + +
81C ALA* 3.6 14.0 - - - +
82C HIS 3.8 6.1 - - - +
83C ALA* 1.3 84.3 - - + +
85C ARG* 1.3 67.9 + - - +
86C PRO* 3.3 12.7 - - + +
89C ASP* 3.5 24.0 - - + +
91C VAL* 3.4 33.2 - - + -
100C LEU* 5.7 0.4 - - + -
104C LEU* 3.8 15.9 - - + -
168C VAL* 5.7 0.2 - - + -
170C VAL* 3.6 32.5 - - + -
247C VAL* 5.6 0.4 - - + -
248C LYS* 6.1 0.4 - - - -
251C VAL* 4.1 10.5 - - + -
255C ARG* 4.8 1.6 - - - +
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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