Contacts of the helix formed by residues 85 - 100 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34I VAL* 4.4 1.5 - - - +
83I CYS* 3.4 12.3 - - - -
84I ARG* 1.3 79.8 - - - +
86I PRO* 1.3 68.8 - - - +
87I MET* 3.0 23.7 + - - +
88I GLN* 3.0 46.1 + - - +
89I VAL 3.6 0.9 + - - -
91I ARG* 4.0 12.6 + - - -
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Residues in contact with PRO 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA 5.5 0.4 - - - +
30I VAL* 3.7 21.8 - - + +
31I ASP* 3.5 26.9 - - - +
34I VAL* 4.0 19.7 - - + -
84I ARG 3.7 7.9 - - - +
85I ASP* 1.3 89.0 - - - +
87I MET* 1.3 64.7 + - + +
89I VAL* 3.1 7.8 + - + +
90I LEU* 3.0 30.3 + - + +
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Residues in contact with MET 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I ASP* 3.0 15.5 + - - +
86I PRO* 1.3 82.4 - - + +
88I GLN* 1.3 57.2 + - - +
90I LEU* 3.3 27.5 + - + +
91I ARG* 2.9 57.1 + - + +
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Residues in contact with GLN 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I MET* 3.6 29.2 - - + +
83I CYS* 4.2 15.9 - - - +
84I ARG 5.5 0.4 - - - +
85I ASP* 3.0 32.9 + - + +
87I MET* 1.3 76.4 - - - +
89I VAL* 1.3 64.4 + - - +
91I ARG* 3.5 25.0 + - - +
92I GLU* 3.1 20.9 + - + +
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Residues in contact with VAL 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I VAL* 3.7 28.5 - - + -
33I ILE* 5.5 0.7 - - + -
34I VAL* 5.1 2.5 - - + -
40I PRO* 3.7 32.5 - - + -
42I LEU* 4.8 1.3 - - + +
80I MET* 4.0 12.3 - - - -
83I CYS* 3.9 15.3 - - - -
85I ASP 4.0 2.2 - - - +
86I PRO* 3.1 10.5 + - + +
88I GLN* 1.3 72.3 - - - +
90I LEU* 1.3 60.7 + - - +
92I GLU* 3.1 4.3 + - - +
93I ILE* 2.9 30.0 + - + +
107I LEU* 3.8 30.1 - - + -
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Residues in contact with LEU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ASP 5.7 0.9 - - - +
26I ILE* 4.4 11.9 - - + -
27I ALA* 4.5 23.1 - - + +
30I VAL* 4.1 23.6 - - + -
86I PRO* 3.0 19.0 + - + +
87I MET* 3.7 37.2 - - + +
89I VAL* 1.3 74.1 - - - +
91I ARG* 1.3 61.6 + - + +
93I ILE* 3.3 17.4 + - + +
94I VAL* 3.1 27.6 + - + +
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Residues in contact with ARG 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I ASP* 4.0 9.1 + - - -
87I MET* 2.9 51.9 + - + +
88I GLN* 3.7 34.4 - - + +
90I LEU* 1.3 77.8 - - + +
92I GLU* 1.3 59.3 + - + +
94I VAL* 3.4 10.0 + - + +
95I ALA* 2.9 27.2 + - - +
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Residues in contact with GLU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I LEU* 3.4 15.8 - - + +
76I TRP* 2.8 30.4 + - + +
77I LYS* 3.0 28.7 + - - +
80I MET* 3.8 26.2 - - + -
88I GLN* 3.1 16.5 + - + +
89I VAL 3.1 10.2 + - - +
91I ARG* 1.3 74.3 - - - +
93I ILE* 1.3 62.0 + - - +
95I ALA* 3.7 6.1 - - - +
96I CYS* 2.8 32.6 + - - +
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Residues in contact with ILE 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ILE* 4.5 12.3 - - + -
30I VAL* 4.8 0.2 - - + -
42I LEU* 3.7 26.2 - - + -
89I VAL* 2.9 30.9 + - + +
90I LEU* 3.3 28.2 + - + +
92I GLU* 1.3 75.8 - - - +
94I VAL* 1.3 63.4 + - + +
96I CYS* 3.8 1.0 - - - +
97I THR* 2.8 37.4 + - + +
107I LEU* 4.5 15.0 - - + -
123I VAL* 4.3 26.0 - - + +
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Residues in contact with VAL 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I LEU 3.1 15.0 + - - +
91I ARG* 3.6 11.4 - - - +
92I GLU 3.3 0.2 - - - -
93I ILE* 1.3 78.1 - - + +
95I ALA* 1.3 62.8 + - - +
97I THR* 3.1 8.0 + - - -
98I LYS* 3.0 34.0 + - + +
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Residues in contact with ALA 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I TRP* 3.7 16.8 - - + -
77I LYS* 4.8 5.2 - - - +
91I ARG 2.9 16.6 + - - +
92I GLU* 3.8 13.0 - - - +
94I VAL* 1.3 78.1 - - - +
96I CYS* 1.3 62.8 + - - +
98I LYS* 3.5 7.7 + - - +
99I ALA* 3.1 23.9 + - - +
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Residues in contact with CYS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I LEU* 4.1 8.7 - - + -
44I PHE* 4.2 12.1 - - - -
76I TRP* 3.6 47.3 - - + -
92I GLU 2.8 20.8 + - - +
93I ILE* 3.8 3.4 - - - +
95I ALA* 1.3 73.8 - - - +
97I THR* 1.3 58.0 + - - +
99I ALA* 3.2 3.8 + - - +
100I PHE* 2.9 29.5 + - - +
105I VAL* 3.8 30.1 - - + -
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Residues in contact with THR 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ILE* 2.8 31.3 + - + +
94I VAL* 3.1 12.1 + - - -
96I CYS* 1.3 71.4 - - - +
98I LYS* 1.3 59.6 + - - +
100I PHE 4.2 5.2 - - - -
101I PRO* 3.1 32.2 - - - +
105I VAL* 4.1 13.0 - - + -
123I VAL* 5.2 1.6 - - + +
124I GLN* 3.2 42.0 - - + +
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Residues in contact with LYS 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I VAL* 3.0 27.5 + - + +
95I ALA* 3.6 8.5 - - - +
97I THR* 1.3 77.8 + - - +
99I ALA* 1.3 62.7 + - - +
101I PRO* 3.4 13.7 - - - +
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Residues in contact with ALA 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I TRP* 3.7 25.8 - - + -
95I ALA 3.1 17.4 + - - +
96I CYS 3.8 1.6 - - - +
98I LYS* 1.3 76.7 - - - +
100I PHE* 1.3 71.1 + - + +
101I PRO* 3.4 6.0 - - - +
140P VAL* 3.9 23.9 - - + +
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Residues in contact with PHE 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I PHE* 3.5 47.8 - + + -
76I TRP* 3.9 13.2 - + - -
96I CYS* 2.9 14.3 + - - +
97I THR* 3.2 5.2 - - - +
99I ALA* 1.3 87.8 - - + +
101I PRO* 1.3 61.1 - - - +
102I ASP 3.2 4.0 + - - -
103I ALA* 3.3 21.7 + - + +
105I VAL* 4.6 1.9 - - + +
124I GLN* 2.9 19.4 + - - -
3P VAL* 4.4 2.0 - - + -
5P THR* 3.6 28.3 - - - -
6P PRO* 4.0 5.2 - - + -
7P VAL* 4.5 13.5 - - + -
140P VAL* 3.7 31.2 - - + -
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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