Contacts of the strand formed by residues 17 - 28 (chain C) in PDB entry 1EQR
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 GLN 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C THR* 4.1 5.9 + - - +
15C GLY 3.9 0.8 + - - -
16C GLN* 1.3 80.3 + - - +
18C VAL* 1.3 73.3 + - - +
19C THR* 5.5 1.6 - - - +
72C THR* 3.9 15.1 + - - +
73C GLY* 3.0 12.9 + - - +
74C THR* 4.3 6.5 - - - +
97C SER* 4.9 6.9 + - - -
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR* 3.5 14.4 - - - +
4C GLU* 4.7 6.5 - - + +
9C LEU* 4.7 11.4 - - + -
13C HIS* 5.6 0.9 - - + -
16C GLN* 4.2 11.0 - - + +
17C GLN* 1.3 82.7 - - - +
19C THR* 1.3 66.7 + - - +
20C LEU* 4.0 31.6 - - + -
71C VAL 5.3 0.2 - - - +
72C THR* 3.0 5.7 + - - -
73C GLY 2.7 41.8 + - - +
75C VAL* 3.8 22.7 - - + -
94C VAL* 4.3 15.7 - - + -
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 3.8 18.8 - - - +
2C ARG* 2.9 7.3 - - - +
3C THR* 2.8 45.9 + - - +
4C GLU 3.8 3.6 + - - +
17C GLN* 5.5 1.9 - - - +
18C VAL* 1.3 78.8 + - - +
20C LEU* 1.3 62.4 + - - +
70C GLN* 3.7 35.7 - - + +
71C VAL 3.6 3.4 - - - -
72C THR* 3.5 12.9 + - - +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ARG* 4.3 0.9 - - - -
4C GLU* 3.6 24.0 - - + +
5C TYR 4.0 1.1 - - - -
6C CYS* 3.7 21.5 - - - +
9C LEU* 4.0 17.7 - - + -
18C VAL* 4.0 15.7 - - + -
19C THR* 1.3 77.5 - - - +
21C CYS* 1.3 61.4 + - - +
38C MET* 3.6 21.3 - - - +
45C VAL* 3.7 28.9 - - + -
47C VAL* 5.7 0.7 - - + -
70C GLN* 3.2 9.9 - - - +
71C VAL* 2.8 40.3 + - + +
94C VAL* 4.2 13.9 - - + -
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Residues in contact with CYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.1 47.3 - - - -
2C ARG* 2.9 51.8 + - - +
4C GLU 5.2 0.2 + - - -
6C CYS* 4.9 1.7 - - - -
20C LEU* 1.3 77.6 - - - +
22C GLY* 1.3 59.2 + - - +
23C TRP* 4.5 1.7 - - - -
38C MET* 3.6 0.9 - - - -
40C ASP* 3.7 9.7 + - - +
68C CYS* 6.1 0.7 - - - -
69C ILE 3.5 4.3 - - - +
70C GLN* 4.1 13.2 - - - -
102C ILE* 4.7 4.5 - - + -
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C CYS* 1.3 75.1 - - - +
23C TRP* 1.3 72.5 + - - -
38C MET* 3.0 13.4 - - - +
39C ARG 3.2 13.0 - - - -
68C CYS* 3.3 7.3 - - - -
69C ILE* 2.7 41.7 + - - +
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Residues in contact with TRP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ARG* 5.3 4.3 - - - -
21C CYS 4.5 2.9 - - - -
22C GLY* 1.3 85.6 - - - -
24C VAL* 1.3 63.3 + - - +
25C ASN 3.3 0.7 + - - -
38C MET* 3.6 6.6 - - - -
39C ARG* 2.9 73.0 + - - +
40C ASP* 4.3 12.3 - - + -
41C ARG 5.2 1.3 - - - -
66C GLU* 3.5 35.9 - - - +
67C PHE 3.1 4.9 - - - +
68C CYS* 3.7 29.5 - - + +
69C ILE* 5.1 1.6 - - - -
130C ARG* 4.5 18.3 - - - +
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TRP* 1.3 70.9 - - - +
25C ASN* 1.3 61.8 + - - +
26C ARG 4.0 15.0 - - - +
27C ARG* 4.4 4.7 - - + -
36C ILE* 3.8 27.6 - - + -
37C ASP 4.1 2.7 - - - -
63C LEU* 4.2 15.5 - - + -
64C ARG 3.2 32.8 - - - +
65C ASN* 3.6 2.9 - - - +
66C GLU* 2.6 34.4 + - - +
67C PHE* 2.9 27.3 + - + +
69C ILE* 4.2 18.4 - - + -
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Residues in contact with ASN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TRP 3.3 0.8 + - - -
24C VAL* 1.3 73.9 - - - +
26C ARG* 1.3 69.6 - - - +
37C ASP* 3.0 21.8 + - + +
39C ARG* 2.7 40.5 + - + +
44C ILE* 3.2 31.7 - - + +
65C ASN* 4.0 11.1 + - - +
66C GLU* 4.3 3.6 - - - +
112C SER* 6.2 0.5 - - - -
132C PRO* 4.9 5.6 - - - +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 3.5 4.9 - - - +
25C ASN* 1.3 90.7 - - - +
27C ARG* 1.3 62.7 + - - +
28C ARG* 4.1 38.1 - - - +
35C PHE* 4.5 13.3 + - - +
36C ILE* 3.6 6.0 - - - -
37C ASP* 2.8 72.2 + - - +
46C GLN* 4.2 16.4 + - - -
65C ASN* 3.8 9.0 - - - +
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Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.4 7.2 - - + -
26C ARG* 1.3 74.9 - - - +
28C ARG* 1.3 100.6 + - - +
29C ASP* 2.7 39.4 + - - +
34C ILE* 3.7 18.7 - - + +
35C PHE 3.4 4.5 - - - +
36C ILE* 3.5 29.8 - - + -
60C ALA 3.4 4.8 + - - -
61C SER* 2.9 34.1 + - - +
63C LEU 2.9 28.4 + - - +
64C ARG* 5.6 1.8 - - - +
65C ASN* 4.1 8.1 - - - +
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ARG* 4.1 37.7 - - - +
27C ARG* 1.3 106.4 + - - +
29C ASP* 1.3 65.4 + - - +
30C LEU* 5.5 1.1 - - + +
35C PHE* 3.0 40.5 + - + +
65C ASN* 5.9 1.4 - - - +
113C ASN* 5.0 12.7 + - - +
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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