Contacts of the helix formed by residues 90 - 103 (chain A) in PDB entry 1R18
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 GLY 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.8 7.2 - - - -
87A SER* 2.7 23.8 + - - -
88A GLY 3.2 0.6 - - - -
89A SER* 1.3 73.8 + - - +
91A TYR* 1.3 62.5 + - - +
92A LEU 3.6 1.3 - - - -
93A THR* 3.4 15.8 + - - -
94A ALA* 3.1 22.9 + - - +
124A SER* 4.2 9.2 - - - -
128A LEU* 3.8 10.4 - - - +
143A ILE* 5.3 1.6 - - - -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 5.0 1.6 + - - -
14A ILE* 5.0 1.7 - - - +
32A MET* 3.8 24.6 + - + +
35A THR* 3.3 39.2 + - + -
37A ARG* 3.7 28.5 - - + +
40A TYR* 3.5 29.3 - + + -
59A ILE* 4.2 6.5 - - + -
65A HIS* 3.2 43.7 - + + -
87A SER 4.6 0.6 + - - -
89A SER* 3.2 17.2 + - - +
90A GLY* 1.3 74.0 - - - +
92A LEU* 1.3 68.9 + - - +
94A ALA* 3.0 14.4 + - - +
95A CYS* 3.0 34.4 + - - -
300A SAH 4.3 1.1 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 4.2 33.9 - - + +
68A ALA* 4.4 7.0 - - + -
69A LEU* 4.1 20.6 - - + -
84A ASP* 4.2 9.4 - - - +
87A SER 5.7 0.4 + - - -
90A GLY 3.6 0.2 - - - -
91A TYR* 1.3 82.3 - - - +
93A THR* 1.3 61.4 + - - +
95A CYS* 3.2 8.3 + - + +
96A PHE* 3.1 51.3 + - + -
162A HIS* 3.4 43.7 - - + +
300A SAH 4.5 10.6 + - - +
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 2.8 24.2 + - + +
87A SER* 4.0 7.6 + - - -
90A GLY* 3.5 20.4 + - - -
91A TYR 3.0 0.2 - - - -
92A LEU* 1.3 75.7 - - - +
94A ALA* 1.3 64.7 + - - +
96A PHE* 3.3 10.3 + - - +
97A TYR* 3.3 20.3 + - - +
111A ILE* 3.5 14.8 - - + +
113A GLY* 4.5 9.6 - - - -
128A LEU* 5.4 0.7 - - - -
141A LEU* 3.3 32.4 - - + +
143A ILE* 4.4 13.4 - - + +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 4.0 13.0 - - + -
40A TYR* 3.5 24.9 - - + +
90A GLY 3.1 10.0 + - - +
91A TYR 3.0 9.0 + - - +
93A THR* 1.3 76.9 - - - +
95A CYS* 1.3 61.4 + - - +
97A TYR* 3.5 4.5 + - - +
98A ARG* 3.1 29.2 + - - +
128A LEU* 3.9 10.3 - - + +
135A MET* 4.2 16.6 - - + +
141A LEU* 4.7 1.1 - - - -
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Residues in contact with CYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.8 10.1 - - + +
32A MET* 4.2 15.5 - - - -
35A THR* 4.0 17.0 - - - -
69A LEU* 4.2 20.4 - - + +
91A TYR* 3.0 50.1 + - - +
92A LEU* 3.4 12.1 - - + +
93A THR 3.2 0.2 - - - -
94A ALA* 1.3 76.4 - - - +
96A PHE* 1.3 60.5 + - - +
98A ARG* 3.4 1.6 + - - -
99A TYR* 2.9 30.5 + - - +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 5.3 1.6 - - + -
69A LEU* 3.5 31.0 - - + -
72A LEU* 4.5 12.3 - - + -
76A LEU* 4.1 24.0 - - + -
82A ILE* 3.6 26.9 - - + -
84A ASP* 4.1 17.3 - - + -
92A LEU* 3.1 45.0 + - + -
93A THR* 3.3 13.0 + - - +
95A CYS* 1.3 75.6 - - - +
97A TYR* 1.3 64.2 + - - +
99A TYR* 3.3 5.9 + - - +
100A ILE* 3.1 28.3 + - + +
111A ILE* 4.3 18.2 - - + -
162A HIS* 4.1 17.3 - + + -
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR 3.3 9.4 + - - +
94A ALA* 3.5 10.8 - - - +
96A PHE* 1.3 80.4 - - - +
98A ARG* 1.3 64.4 + - + +
100A ILE* 3.9 1.6 - - - +
101A LYS* 2.9 53.8 + - + +
109A THR* 6.0 0.7 - - + -
111A ILE* 4.3 23.5 - - + +
132A ASP* 5.8 0.7 - - - -
134A SER* 4.2 3.9 + - - -
135A MET* 3.5 41.7 + - + -
138A SER* 3.5 32.8 + - - -
140A GLN* 4.0 20.8 + - + -
141A LEU* 4.2 19.3 - - + -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.5 12.5 - - - +
34A GLU* 3.2 45.6 + - - +
35A THR* 3.0 29.8 + - - +
94A ALA* 3.1 16.3 + - - +
95A CYS 4.0 2.7 - - - +
97A TYR* 1.3 82.4 - - + +
99A TYR* 1.3 66.8 + - - +
101A LYS* 3.6 15.6 + - + +
102A ALA* 3.1 23.4 + - - +
131A ASP* 2.9 41.2 + - - -
132A ASP* 3.7 22.6 + - - +
135A MET* 4.0 12.9 - - - +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 5.0 0.7 + - - -
27A ALA* 3.6 41.4 - - + +
28A VAL* 3.7 22.5 - - + +
31A ALA* 3.9 12.7 - - + +
69A LEU* 5.0 5.2 - - + -
73A ARG* 3.3 35.8 + - + +
76A LEU* 3.6 47.8 - - + -
95A CYS 2.9 18.3 + - - +
96A PHE* 3.5 8.3 - - - +
98A ARG* 1.3 77.9 - - - +
100A ILE* 1.3 61.5 + - - +
102A ALA* 3.4 12.0 + - - +
103A LYS* 3.5 35.3 + - - +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.7 34.3 - - + +
77A LYS 4.1 7.6 - - - +
78A PRO* 3.7 28.5 - - + -
82A ILE* 3.8 30.3 - - + -
96A PHE 3.1 15.5 + - - +
97A TYR* 4.1 3.4 - - - +
99A TYR* 1.3 74.6 - - - +
101A LYS* 1.3 67.7 + - - +
102A ALA 3.0 2.2 - - - -
103A LYS* 2.9 21.2 + - - +
104A GLY 3.0 16.3 + - - +
105A VAL* 6.1 0.2 - - - -
109A THR* 4.0 26.0 - - + +
111A ILE* 4.4 5.8 - - + -
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 5.0 9.3 + - - -
97A TYR* 2.9 47.8 + - + +
98A ARG* 3.3 15.7 + - + +
100A ILE* 1.3 77.6 - - - +
102A ALA* 1.3 61.1 + - - +
104A GLY* 3.4 17.1 + - - -
105A VAL* 4.4 8.6 + - + +
132A ASP* 6.0 2.0 - - - -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 6.5 1.1 - - + -
30A GLN* 6.4 2.5 - - + -
34A GLU* 6.0 2.5 - - - +
98A ARG 3.1 11.4 + - - +
99A TYR* 3.5 10.8 - - - +
100A ILE 3.0 0.8 - - - -
101A LYS* 1.3 75.0 - - - +
103A LYS* 1.3 59.6 + - + +
104A GLY* 2.9 11.3 + - - -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.2 14.6 - - - +
73A ARG 5.4 1.3 - - - -
76A LEU 4.3 11.4 - - - +
78A PRO* 3.7 24.7 - - + +
99A TYR* 3.5 45.0 + - + +
100A ILE* 2.9 13.0 + - - +
102A ALA* 1.3 75.8 - - + +
104A GLY* 1.3 57.6 + - - +
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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