Contacts of the helix formed by residues 85 - 100 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34W VAL* 4.4 1.1 - - - -
83W CYS* 3.4 11.5 - - - -
84W ARG* 1.3 79.8 - - - +
86W PRO* 1.3 70.2 - - - +
87W MET* 3.0 23.4 + - - +
88W GLN* 3.0 41.5 + - - +
89W VAL 3.6 0.9 + - - -
91W ARG* 4.0 17.0 + - - -
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Residues in contact with PRO 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27W ALA 5.5 0.4 - - - +
30W VAL* 3.7 22.0 - - + +
31W ASP* 3.5 26.2 - - - +
34W VAL* 4.0 18.5 - - + -
84W ARG 3.7 8.3 - - - +
85W ASP* 1.3 89.8 - - - +
87W MET* 1.3 64.1 + - + +
89W VAL* 3.1 6.7 + - + +
90W LEU* 3.0 30.5 + - + +
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Residues in contact with MET 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85W ASP* 3.0 15.7 + - - +
86W PRO* 1.3 83.0 - - + +
88W GLN* 1.3 57.4 + - - +
90W LEU* 3.4 27.1 + - + +
91W ARG* 2.9 56.5 + - + +
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Residues in contact with GLN 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80W MET* 3.7 18.1 - - + +
83W CYS* 4.1 19.2 - - - +
84W ARG 5.5 0.6 - - - +
85W ASP* 3.0 31.5 + - + +
87W MET* 1.3 77.4 - - - +
89W VAL* 1.3 64.2 + - - +
91W ARG* 3.5 26.3 + - - +
92W GLU* 3.1 28.0 + - + +
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Residues in contact with VAL 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W VAL* 3.8 29.8 - - + -
33W ILE* 5.4 0.9 - - + -
34W VAL* 5.1 2.9 - - + -
40W PRO* 3.7 32.5 - - + -
42W LEU* 5.9 1.3 - - + -
80W MET* 4.0 11.2 - - + -
83W CYS* 4.0 8.3 - - - -
85W ASP 4.0 9.0 - - - +
86W PRO* 3.1 11.1 + - + +
88W GLN* 1.3 75.0 - - - +
90W LEU* 1.3 56.9 + - - +
92W GLU* 3.1 5.0 + - - +
93W ILE* 3.0 30.6 + - + +
107W LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23W ASP 5.7 0.7 - - - +
26W ILE* 4.3 13.0 - - + -
27W ALA* 4.4 22.2 - - + +
30W VAL* 4.1 23.8 - - + -
86W PRO* 3.0 18.6 + - + +
87W MET* 3.7 37.2 - - + +
88W GLN 3.3 0.2 - - - -
89W VAL* 1.3 74.8 - - - +
91W ARG* 1.3 62.2 + - + +
93W ILE* 3.3 16.8 + - + +
94W VAL* 3.1 26.9 + - - +
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Residues in contact with ARG 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85W ASP* 4.0 8.9 + - - -
87W MET* 2.9 47.2 + - + +
88W GLN* 3.6 35.8 - - - +
90W LEU* 1.3 78.1 - - - +
92W GLU* 1.3 58.0 + - - +
94W VAL* 3.3 10.5 + - + +
95W ALA* 3.0 26.7 + - - +
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Residues in contact with GLU 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42W LEU* 3.5 16.1 - - + +
76W TRP* 2.8 31.7 + - + +
77W LYS* 3.0 29.3 + - - +
80W MET* 3.8 26.2 - - + +
88W GLN* 3.1 15.4 + - + +
89W VAL 3.1 9.1 + - - +
91W ARG* 1.3 74.1 - - - +
93W ILE* 1.3 61.4 + - - +
95W ALA* 3.8 5.4 - - - +
96W CYS* 2.8 33.3 + - - +
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Residues in contact with ILE 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W ILE* 4.5 12.1 - - + -
30W VAL* 4.8 0.2 - - + -
42W LEU* 3.6 26.9 - - + +
89W VAL* 3.0 30.5 + - + +
90W LEU* 3.3 27.8 + - + +
92W GLU* 1.3 75.6 - - - +
94W VAL* 1.3 62.8 + - + +
96W CYS* 3.4 1.2 + - - +
97W THR* 2.8 38.8 + - + +
105W VAL* 5.8 0.2 - - + -
107W LEU* 4.5 15.0 - - + -
123W VAL* 4.3 26.5 - - + +
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Residues in contact with VAL 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90W LEU 3.1 16.7 + - - +
91W ARG* 3.5 9.9 - - + +
93W ILE* 1.3 78.5 - - + +
95W ALA* 1.3 58.2 + - - +
97W THR* 3.2 7.2 + - - -
98W LYS* 3.0 37.2 + - + +
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Residues in contact with ALA 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W TRP* 3.6 16.3 - - + -
77W LYS* 4.8 4.3 - - - +
91W ARG 3.0 17.1 + - - +
92W GLU* 3.8 13.5 - - - +
94W VAL* 1.3 78.9 - - - +
96W CYS* 1.3 62.1 + - - +
98W LYS* 3.4 7.9 + - - +
99W ALA* 3.1 24.4 + - - +
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Residues in contact with CYS 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42W LEU* 4.1 7.2 - - + -
44W PHE* 4.3 12.3 - - - -
76W TRP* 3.6 47.0 - - + -
92W GLU 2.8 21.4 + - - +
93W ILE* 3.8 3.4 - - - +
95W ALA* 1.3 73.2 - - - +
97W THR* 1.3 56.9 + - - +
99W ALA* 3.2 3.8 + - - +
100W PHE* 2.9 28.8 + - - +
105W VAL* 3.7 34.1 - - + -
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Residues in contact with THR 97 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93W ILE* 2.8 34.0 + - + +
94W VAL* 3.2 11.8 + - - -
96W CYS* 1.3 75.3 - - - +
98W LYS* 1.3 59.3 + - - +
100W PHE 4.1 4.9 - - - -
101W PRO* 3.1 27.7 - - - +
105W VAL* 4.2 14.1 - - + -
123W VAL* 5.1 1.6 - - + +
124W GLN* 3.1 43.8 - - + +
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Residues in contact with LYS 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94W VAL* 3.0 26.4 + - + +
95W ALA* 3.7 7.9 - - - +
96W CYS 3.2 0.4 - - - -
97W THR* 1.3 76.3 + - - +
99W ALA* 1.3 62.5 + - - +
101W PRO* 3.4 13.8 - - - +
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Residues in contact with ALA 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J VAL* 3.9 24.9 - - + +
76W TRP* 3.7 25.1 - - + -
95W ALA 3.1 16.6 + - - +
96W CYS 3.2 1.8 + - - +
98W LYS* 1.3 77.1 - - - +
100W PHE* 1.3 71.0 + - + +
101W PRO* 3.4 6.9 - - - +
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Residues in contact with PHE 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J VAL* 4.4 2.5 - - + -
5J THR* 3.5 30.5 - - - -
6J PRO* 4.0 3.1 - - + -
7J VAL* 4.5 12.8 - - + -
140J VAL* 3.6 31.6 - - + -
44W PHE* 3.5 46.4 - + + -
76W TRP* 3.9 15.5 - + - -
96W CYS* 2.9 10.9 + - - +
97W THR* 3.3 6.0 - - - +
99W ALA* 1.3 87.6 - - + +
101W PRO* 1.3 61.2 - - - +
102W ASP 3.2 4.1 + - - -
103W ALA* 3.3 21.6 + - + +
105W VAL* 4.5 1.9 - - + +
124W GLN* 2.9 20.1 + - - -
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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