Contacts of the helix formed by residues 85 - 100 (chain M) in PDB entry 1UW9
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 ASP 85 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34M VAL* 4.4 1.5 - - - +
83M CYS* 3.4 11.2 - - - -
84M ARG* 1.3 80.7 - - - +
86M PRO* 1.3 67.6 - - - +
87M MET* 3.0 24.3 + - - +
88M GLN* 3.0 42.2 + - - +
89M VAL 3.5 0.9 + - - -
91M ARG* 3.9 17.2 + - - -
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Residues in contact with PRO 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ALA 5.5 0.2 - - - +
30M VAL* 3.7 22.5 - - + +
31M ASP* 3.5 26.5 - - - +
34M VAL* 4.0 19.7 - - + -
84M ARG 3.8 8.1 - - - +
85M ASP* 1.3 89.4 - - - +
87M MET* 1.3 65.8 + - + +
89M VAL* 3.0 15.7 + - + +
90M LEU* 3.1 20.2 + - + +
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Residues in contact with MET 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M ASP* 3.0 15.4 + - - +
86M PRO* 1.3 80.8 - - + +
88M GLN* 1.3 56.3 + - - +
90M LEU* 3.3 27.7 + - + +
91M ARG* 2.9 56.2 + - + +
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Residues in contact with GLN 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M MET* 3.7 21.8 - - + +
83M CYS* 4.1 15.7 - - - +
84M ARG 5.4 0.4 - - - +
85M ASP* 3.0 33.5 + - + +
87M MET* 1.3 79.2 - - - +
89M VAL* 1.3 62.0 + - - +
91M ARG* 3.4 25.0 + - - +
92M GLU* 3.1 28.1 + - + +
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Residues in contact with VAL 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL* 3.7 27.8 - - + -
33M ILE* 5.5 1.1 - - + -
34M VAL* 5.1 2.5 - - + -
40M PRO* 3.7 32.5 - - + -
42M LEU* 5.9 1.1 - - + -
80M MET* 4.0 11.7 - - - -
83M CYS* 3.9 15.3 - - - -
85M ASP 4.0 2.0 - - - +
86M PRO* 3.0 10.5 + - + +
88M GLN* 1.3 76.8 - - - +
90M LEU* 1.3 57.2 + - - +
92M GLU* 3.1 5.2 + - + +
93M ILE* 3.0 30.9 + - + +
107M LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M ASP 5.6 0.9 - - - +
26M ILE* 4.3 11.9 - - + -
27M ALA* 4.4 22.7 - - + +
30M VAL* 4.1 22.7 - - + -
86M PRO* 3.1 19.1 + - + +
87M MET* 3.7 37.0 - - + +
89M VAL* 1.3 74.9 - - - +
91M ARG* 1.3 62.7 + - + +
93M ILE* 3.3 18.7 + - + +
94M VAL* 3.2 26.9 + - + +
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M ASP* 3.9 9.7 + - - -
87M MET* 2.9 48.3 + - + +
88M GLN* 3.6 33.5 - - - +
90M LEU* 1.3 76.6 - - + +
92M GLU* 1.3 59.5 + - + +
94M VAL* 3.3 10.4 + - + +
95M ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LEU* 3.5 15.2 - - + +
76M TRP* 2.8 32.2 + - + +
77M LYS* 2.9 30.0 + - - +
80M MET* 3.8 26.2 - - + -
88M GLN* 3.1 18.9 + - + +
89M VAL 3.1 8.0 + - - +
91M ARG* 1.3 75.8 - - - +
93M ILE* 1.3 60.9 + - - +
95M ALA* 3.8 5.2 - - - +
96M CYS* 2.8 32.6 + - - +
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Residues in contact with ILE 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M ILE* 4.6 11.7 - - + -
30M VAL* 4.8 0.2 - - + -
42M LEU* 3.7 26.5 - - + -
89M VAL* 3.0 23.5 + - + +
90M LEU* 3.3 27.6 + - + +
92M GLU* 1.3 75.1 - - - +
94M VAL* 1.3 64.9 + - + +
96M CYS* 3.9 0.6 - - - +
97M THR* 2.8 38.4 + - + +
107M LEU* 4.4 21.5 - - + -
123M VAL* 4.3 26.5 - - + +
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Residues in contact with VAL 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90M LEU* 3.2 16.9 + - + +
91M ARG* 3.5 11.0 - - - +
92M GLU 3.2 0.2 - - - -
93M ILE* 1.3 78.4 - - + +
95M ALA* 1.3 58.0 + - - +
97M THR* 3.1 8.2 + - - +
98M LYS* 2.9 39.8 + - + +
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Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M TRP* 3.7 16.2 - - + -
77M LYS* 4.8 4.3 - - - +
91M ARG 3.0 16.9 + - - +
92M GLU* 3.2 13.4 + - - +
94M VAL* 1.3 76.1 - - - +
96M CYS* 1.3 63.4 + - - +
98M LYS* 3.4 8.4 + - - +
99M ALA* 3.0 24.8 + - - +
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Residues in contact with CYS 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LEU* 4.1 7.4 - - + -
44M PHE* 4.2 12.6 - - - -
76M TRP* 3.6 48.8 - - + -
92M GLU 2.8 21.0 + - - +
93M ILE* 3.9 2.7 - - - +
95M ALA* 1.3 73.1 - - - +
97M THR* 1.3 58.5 + - - +
99M ALA* 3.2 5.0 + - - +
100M PHE* 2.9 29.5 + - - +
105M VAL* 3.8 31.0 - - + -
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Residues in contact with THR 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93M ILE* 2.8 34.4 + - + +
94M VAL* 3.1 12.0 + - - -
96M CYS* 1.3 73.4 - - - +
98M LYS* 1.3 56.5 + - - +
100M PHE 4.1 5.2 - - - -
101M PRO* 3.1 32.7 - - - +
105M VAL* 4.1 14.4 - - + -
123M VAL* 5.1 1.1 - - + +
124M GLN* 3.2 42.0 - - + +
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Residues in contact with LYS 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M VAL* 2.9 27.7 + - + +
95M ALA* 3.6 8.7 - - - +
96M CYS 3.2 0.2 - - - -
97M THR* 1.3 78.5 + - - +
99M ALA* 1.3 61.0 + - - +
101M PRO* 3.5 13.6 - - - +
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Residues in contact with ALA 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M TRP* 3.7 24.9 - - + -
95M ALA 3.0 16.5 + - - +
96M CYS 3.7 3.4 - - - +
98M LYS* 1.3 75.9 - - - +
100M PHE* 1.3 71.9 + - + +
101M PRO* 3.4 6.2 - - - +
140T VAL* 3.9 23.4 - - + +
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Residues in contact with PHE 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M PHE* 3.5 46.9 - + + -
76M TRP* 3.9 12.3 - + - -
96M CYS* 2.9 14.8 + - - +
97M THR* 3.2 5.6 - - - +
99M ALA* 1.3 87.1 - - + +
101M PRO* 1.3 61.8 - - - +
102M ASP 3.2 3.8 + - - -
103M ALA* 3.3 21.7 + - + +
105M VAL* 4.6 1.2 - - + +
124M GLN* 2.9 19.9 + - - -
3T VAL* 4.6 1.6 - - + -
5T THR* 3.5 28.5 - - - -
6T PRO* 3.9 6.1 - - + -
7T VAL* 4.3 15.5 - - + -
140T VAL* 3.8 29.4 - - + -
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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