Contacts of the helix formed by residues 85 - 100 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H THR* 3.9 26.0 + - - +
34P VAL* 4.4 2.0 - - - +
83P CYS* 3.3 9.2 - - - -
84P ARG* 1.3 80.7 - - - +
86P PRO* 1.3 69.0 - - - +
87P MET* 3.0 22.9 + - - +
88P GLN* 3.1 46.0 + - - +
89P VAL* 3.5 1.9 + - - +
91P ARG* 4.1 12.8 + - - -
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Residues in contact with PRO 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H THR* 4.7 6.3 - - + -
27P ALA 5.5 0.4 - - - +
30P VAL* 3.7 21.6 - - + +
31P ASP* 3.5 25.8 - - - +
34P VAL* 4.0 18.1 - - + -
84P ARG 3.7 9.0 - - - +
85P ASP* 1.3 90.7 - - - +
87P MET* 1.3 63.8 + - + +
89P VAL* 3.1 6.9 + - + +
90P LEU* 3.0 29.6 + - + +
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Residues in contact with MET 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ASP* 3.0 14.6 + - - +
86P PRO* 1.3 83.6 - - + +
88P GLN* 1.3 57.0 + - - +
90P LEU* 3.4 27.2 + - + +
91P ARG* 2.9 55.9 + - + +
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Residues in contact with GLN 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H THR 5.7 1.4 + - - -
80P MET* 3.7 18.6 - - + +
83P CYS* 4.0 17.4 - - - +
84P ARG 5.4 0.4 - - - +
85P ASP* 3.1 33.5 + - + +
87P MET* 1.3 75.0 - - - +
89P VAL* 1.3 64.3 + - - +
91P ARG* 3.4 26.0 + - - +
92P GLU* 3.1 27.8 + - + +
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Residues in contact with VAL 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P VAL* 3.7 29.2 - - + -
33P ILE* 5.4 1.3 - - + -
34P VAL* 5.0 2.9 - - + -
40P PRO* 3.7 31.9 - - + -
42P LEU* 4.8 1.5 - - + +
80P MET* 4.0 10.8 - - - -
83P CYS* 4.0 8.3 - - - -
85P ASP 3.9 11.7 - - - +
86P PRO* 3.1 7.3 + - + +
88P GLN* 1.3 76.4 - - - +
90P LEU* 1.3 62.4 + - - +
92P GLU* 3.1 4.9 + - - +
93P ILE* 3.0 24.7 + - + +
107P LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P ASP 5.6 0.9 - - - +
26P ILE* 4.4 11.7 - - + -
27P ALA* 4.5 24.0 - - + +
30P VAL* 4.1 22.0 - - + -
86P PRO* 3.0 23.2 + - + +
87P MET* 3.7 35.0 - - + +
89P VAL* 1.3 74.8 - - - +
91P ARG* 1.3 60.1 - - + +
93P ILE* 3.3 18.1 + - + +
94P VAL* 3.1 26.9 + - - +
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Residues in contact with ARG 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P ASP* 4.1 8.7 + - - -
87P MET* 2.9 50.8 + - + +
88P GLN* 3.6 34.0 - - - +
90P LEU* 1.3 73.9 - - + +
92P GLU* 1.3 62.7 + - - +
94P VAL* 3.3 10.0 + - + +
95P ALA* 2.9 26.9 + - - +
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Residues in contact with GLU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P LEU* 3.4 15.6 - - + +
76P TRP* 2.8 31.9 + - + +
77P LYS* 3.0 28.7 + - - +
80P MET* 3.8 26.9 - - + -
88P GLN* 3.1 16.3 + - + +
89P VAL 3.1 7.8 + - - +
91P ARG* 1.3 75.0 - - - +
93P ILE* 1.3 59.9 + - - +
95P ALA* 3.8 5.6 - - - +
96P CYS* 2.8 32.6 + - - +
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Residues in contact with ILE 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 4.6 11.2 - - + -
42P LEU* 3.8 25.4 - - + -
89P VAL* 3.0 25.2 + - + +
90P LEU* 3.3 27.8 + - + +
92P GLU* 1.3 75.1 - - - +
94P VAL* 1.3 62.8 + - + +
96P CYS* 3.8 1.4 - - - +
97P THR* 2.8 38.1 + - + +
107P LEU* 4.4 22.2 - - + -
123P VAL* 4.2 27.8 - - + +
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Residues in contact with VAL 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P LEU 3.1 16.3 + - - +
91P ARG* 3.6 10.1 - - - +
92P GLU 3.2 0.4 - - - -
93P ILE* 1.3 78.1 - - + +
95P ALA* 1.3 64.6 + - - +
97P THR* 3.1 7.7 + - - -
98P LYS* 2.9 33.8 + - + +
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Residues in contact with ALA 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P TRP* 3.7 16.2 - - + -
77P LYS* 4.9 3.8 - - - +
91P ARG 2.9 17.3 + - - +
92P GLU* 3.8 13.0 - - - +
94P VAL* 1.3 77.7 - - - +
96P CYS* 1.3 62.0 + - - +
98P LYS* 3.4 8.5 + - - +
99P ALA* 3.1 24.4 + - - +
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Residues in contact with CYS 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P LEU* 4.1 7.4 - - + -
44P PHE* 4.3 12.1 - - - -
76P TRP* 3.6 48.8 - - + -
92P GLU 2.8 21.3 + - - +
93P ILE* 3.8 2.9 - - - +
95P ALA* 1.3 73.8 - - - +
97P THR* 1.3 57.4 + - - +
99P ALA* 3.2 4.9 + - - +
100P PHE* 2.9 28.3 + - - +
105P VAL* 3.8 32.5 - - + -
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Residues in contact with THR 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P ILE* 2.8 34.1 + - + +
94P VAL* 3.1 11.8 + - - -
96P CYS* 1.3 74.0 - - - +
98P LYS* 1.3 57.2 + - - +
100P PHE 4.1 5.4 - - - -
101P PRO* 3.1 31.9 - - - +
105P VAL* 4.2 13.2 - - + -
123P VAL* 5.0 1.8 - - + +
124P GLN* 3.1 43.5 - - + +
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Residues in contact with LYS 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P VAL* 2.9 25.3 + - + +
95P ALA* 3.6 8.1 - - - +
97P THR* 1.3 75.8 + - - +
99P ALA* 1.3 63.3 + - - +
101P PRO* 3.5 13.7 - - - +
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Residues in contact with ALA 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M VAL* 3.9 28.0 - - + +
76P TRP* 3.7 26.2 - - + -
95P ALA 3.1 17.0 + - - +
96P CYS 3.7 1.6 - - - +
98P LYS* 1.3 77.0 - - - +
100P PHE* 1.3 68.7 + - + +
101P PRO* 3.5 6.2 - - - +
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Residues in contact with PHE 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M VAL* 4.5 2.7 - - + -
5M THR* 3.4 32.8 - - - -
6M PRO* 4.1 2.2 - - + -
7M VAL* 4.5 12.8 - - + -
140M VAL* 3.5 32.3 - - + -
44P PHE* 3.5 46.9 - + + -
76P TRP* 3.9 13.5 - + - -
96P CYS* 2.9 12.5 + - - +
97P THR* 3.3 6.1 - - - +
99P ALA* 1.3 86.9 - - + +
101P PRO* 1.3 61.3 - - - +
102P ASP 3.2 4.0 + - - -
103P ALA* 3.3 21.8 + - + +
105P VAL* 4.6 1.4 - - + +
124P GLN* 2.9 19.8 + - - -
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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