Contacts of the helix formed by residues 85 - 100 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34T VAL* 4.4 2.0 - - - +
83T CYS* 3.4 11.2 - - - -
84T ARG* 1.3 79.2 - - - +
86T PRO* 1.3 68.9 - - - +
87T MET* 3.0 23.0 + - - +
88T GLN* 3.1 46.4 + - - +
89T VAL 3.5 1.6 + - - -
91T ARG* 4.1 13.0 + - - -
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Residues in contact with PRO 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T ALA 5.5 0.4 - - - +
30T VAL* 3.7 22.3 - - + +
31T ASP* 3.5 25.6 - - - +
34T VAL* 4.0 18.1 - - + -
84T ARG 3.7 9.4 - - - +
85T ASP* 1.3 91.3 - - - +
87T MET* 1.3 59.1 + - + +
89T VAL* 3.1 7.5 + - + +
90T LEU* 3.0 34.7 + - + +
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Residues in contact with MET 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T ASP* 3.0 15.7 + - - +
86T PRO* 1.3 82.0 - - + +
88T GLN* 1.3 58.1 + - - +
90T LEU* 3.3 26.9 + - + +
91T ARG* 2.9 56.0 + - + +
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Residues in contact with GLN 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 5.8 5.9 - - - +
80T MET* 3.8 19.1 - - + +
83T CYS* 4.0 18.3 - - - +
84T ARG 5.5 0.4 - - - +
85T ASP* 3.1 33.9 + - + +
87T MET* 1.3 76.0 - - - +
89T VAL* 1.3 64.0 + - - +
91T ARG* 3.3 25.7 + - - +
92T GLU* 3.0 27.9 + - + +
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Residues in contact with VAL 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T VAL* 3.7 28.3 - - + -
33T ILE* 5.5 1.1 - - + -
34T VAL* 5.0 3.6 - - + -
40T PRO* 3.8 32.3 - - + -
42T LEU* 6.0 1.6 - - + -
80T MET* 4.1 11.2 - - - -
83T CYS* 4.0 8.3 - - - -
85T ASP 3.9 11.9 - - - +
86T PRO* 3.1 7.8 + - + +
88T GLN* 1.3 75.1 - - - +
90T LEU* 1.3 63.9 + - - +
92T GLU* 3.1 5.2 + - - +
93T ILE* 3.0 23.9 + - + +
107T LEU* 3.8 29.6 - - + -
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Residues in contact with LEU 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T ASP 5.7 0.9 - - - +
26T ILE* 4.3 12.1 - - + -
27T ALA* 4.5 22.4 - - + +
30T VAL* 4.1 22.4 - - + -
86T PRO* 3.0 22.7 + - + +
87T MET* 3.7 34.5 - - + +
89T VAL* 1.3 74.0 - - - +
91T ARG* 1.3 62.5 + - + +
93T ILE* 3.3 17.7 + - + +
94T VAL* 3.1 26.6 + - - +
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Residues in contact with ARG 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T ASP* 4.1 8.5 + - - -
87T MET* 2.9 50.3 + - + +
88T GLN* 3.6 33.6 - - - +
89T VAL 3.2 0.2 - - - -
90T LEU* 1.3 76.9 - - + +
92T GLU* 1.3 59.2 + - + +
94T VAL* 3.3 10.4 + - - +
95T ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T LEU* 3.4 15.6 - - + +
76T TRP* 2.8 31.6 + - + +
77T LYS* 3.0 28.9 + - - +
80T MET* 3.8 26.8 - - + +
88T GLN* 3.0 17.3 + - + +
89T VAL 3.1 8.2 + - - +
91T ARG* 1.3 73.2 - - - +
93T ILE* 1.3 60.9 + - - +
95T ALA* 3.8 6.2 - - - +
96T CYS* 2.8 32.7 + - - +
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Residues in contact with ILE 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T ILE* 4.5 12.6 - - + -
30T VAL* 4.8 0.7 - - + -
42T LEU* 3.8 24.7 - - + -
89T VAL* 3.0 22.7 + - + +
90T LEU* 3.3 28.0 + - + +
92T GLU* 1.3 75.6 - - - +
94T VAL* 1.3 57.6 + - + +
96T CYS* 3.9 0.4 - - - +
97T THR* 2.8 44.0 + - + +
107T LEU* 4.4 20.9 - - + -
123T VAL* 4.2 27.1 - - + +
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Residues in contact with VAL 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90T LEU* 3.1 16.0 + - + +
91T ARG* 3.5 10.1 - - - +
92T GLU 3.2 0.2 - - - -
93T ILE* 1.3 78.2 - - + +
95T ALA* 1.3 58.6 + - - +
97T THR* 3.1 7.0 + - - -
98T LYS* 3.0 38.7 + - + +
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Residues in contact with ALA 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76T TRP* 3.6 15.5 - - + -
77T LYS* 4.8 3.8 - - - +
91T ARG 3.0 16.5 + - - +
92T GLU* 3.3 14.1 + - - +
94T VAL* 1.3 76.9 - - - +
96T CYS* 1.3 62.6 + - - +
98T LYS* 3.4 8.9 + - - +
99T ALA* 3.0 24.9 + - - +
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Residues in contact with CYS 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T LEU* 4.1 7.2 - - + -
44T PHE* 4.2 12.6 - - - -
76T TRP* 3.6 47.7 - - + -
92T GLU 2.8 17.9 + - - +
93T ILE* 3.9 3.4 - - - +
95T ALA* 1.3 76.6 - - - +
97T THR* 1.3 58.2 + - - +
99T ALA* 3.2 4.0 + - - +
100T PHE* 2.9 29.8 + - - +
105T VAL* 3.8 30.7 - - + -
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Residues in contact with THR 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93T ILE* 2.8 33.4 + - + +
94T VAL* 3.1 11.8 + - - -
96T CYS* 1.3 72.2 - - - +
98T LYS* 1.3 63.4 + - - +
100T PHE 4.2 5.6 - - - -
101T PRO* 3.1 27.7 - - - +
105T VAL* 4.1 14.6 - - + -
123T VAL* 5.1 1.8 - - + +
124T GLN* 3.2 41.5 - - + +
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Residues in contact with LYS 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94T VAL* 3.0 26.8 + - + +
95T ALA* 3.6 8.3 - - - +
97T THR* 1.3 77.0 + - - +
99T ALA* 1.3 62.6 + - - +
101T PRO* 3.5 14.0 - - - +
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Residues in contact with ALA 99 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I VAL* 3.9 25.2 - - + +
76T TRP* 3.7 24.9 - - + -
95T ALA 3.0 16.8 + - - +
96T CYS 3.7 1.6 - - - +
98T LYS* 1.3 76.5 - - - +
100T PHE* 1.3 71.2 + - + +
101T PRO* 3.4 6.7 - - - +
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Residues in contact with PHE 100 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.4 2.2 - - + -
5I THR* 3.5 30.3 - - - -
6I PRO* 4.1 3.1 - - + -
7I VAL* 4.5 12.3 - - + -
140I VAL* 3.6 32.3 - - + -
44T PHE* 3.5 46.9 - + + -
76T TRP* 3.8 13.0 - + - -
96T CYS 2.9 13.5 + - - +
97T THR* 3.3 5.3 - - - +
99T ALA* 1.3 86.6 - - + +
101T PRO* 1.3 61.1 - - - +
102T ASP 3.2 4.9 + - - -
103T ALA* 3.2 21.6 + - + +
105T VAL* 4.6 2.5 - - + +
124T GLN* 2.9 19.6 + - - -
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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