Contacts of the strand formed by residues 33 - 40 (chain B) 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 LEU 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG 4.0 0.2 - - - +
29B ASP* 3.3 5.7 - - - +
30B LEU* 2.8 65.5 + - + +
32B SER* 1.3 88.5 - - - +
34B ILE* 1.3 59.2 + - - +
35B PHE* 4.0 0.7 + - - -
48B PHE* 3.3 32.3 - - + -
49B PHE 4.0 3.4 - - - -
50B ASP* 2.9 33.9 - - + +
51B PRO* 5.7 1.8 - - + +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 3.4 36.1 - - + +
28B ARG 3.6 2.2 - - - -
29B ASP* 3.6 19.7 - - - +
32B SER 3.5 8.4 + - - +
33B LEU* 1.3 74.4 - - - +
35B PHE* 1.3 63.3 + - - +
36B ILE* 4.6 2.9 - - + -
48B PHE* 3.5 2.1 - - - -
49B PHE* 2.9 58.0 + - + -
57B LEU* 4.3 7.6 - - + -
60B ALA* 3.2 31.2 - - + +
61B SER* 3.2 27.4 - - - +
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 5.7 4.8 + - - +
27B ARG* 3.4 3.8 - - - +
28B ARG* 2.7 55.6 + - + +
29B ASP 5.3 0.4 - - - -
30B LEU* 4.3 30.3 - - + -
33B LEU 4.6 4.5 - - - -
34B ILE* 1.3 72.1 - - - +
36B ILE* 1.3 63.4 + - - +
46B GLN* 3.6 36.8 - - + -
47B VAL 3.6 1.1 - - - -
48B PHE* 3.2 57.7 - + + -
93B GLU* 4.4 4.3 - - - -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.3 23.6 - - + -
26B ARG* 3.2 13.2 - - - +
27B ARG* 3.1 33.9 - - + -
34B ILE* 4.6 0.7 - - + -
35B PHE* 1.3 72.9 - - - +
37B ASP* 1.3 62.6 + - - +
38B MET* 3.3 14.3 + - + +
46B GLN* 3.5 4.7 - - - +
47B VAL* 2.7 66.0 + - + +
49B PHE* 4.4 6.7 - - + -
63B LEU* 3.2 37.0 - - + -
69B ILE* 5.8 1.8 - - + -
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.8 0.3 - - - -
25B ASN* 2.7 42.9 + - + +
26B ARG* 3.0 56.5 + - + +
36B ILE* 1.3 70.9 - - - +
38B MET* 1.3 56.8 + - - +
44B ILE* 3.5 22.9 - - + +
45B VAL 3.8 1.3 - - - -
46B GLN* 4.3 13.0 - - - +
87B MET* 4.3 17.9 - - - +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS* 3.5 12.4 - - - -
20B LEU* 3.1 46.7 - - + +
21B CYS 3.8 0.9 - - - -
22B GLY* 3.5 18.8 - - - +
23B TRP 3.4 13.2 - - - +
36B ILE* 3.3 5.5 + - + -
37B ASP* 1.3 71.2 - - - +
39B ARG* 1.3 61.8 + - - +
44B ILE* 3.5 1.2 - - - -
45B VAL* 2.8 47.8 + - + +
47B VAL* 3.8 17.7 - - + -
69B ILE* 3.5 29.4 - - + +
71B VAL* 4.1 20.0 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLY* 5.8 3.6 - - - -
6B CYS* 4.4 0.9 - - - -
22B GLY* 3.2 4.4 - - - -
23B TRP* 2.6 68.9 + - - +
24B VAL 4.3 0.8 + - - -
25B ASN* 2.9 32.0 + - + +
37B ASP 3.5 0.6 + - - -
38B MET* 1.3 75.1 - - - +
40B ASP* 1.3 76.9 + - - +
43B GLY 3.7 7.6 - - - +
44B ILE* 4.0 18.2 - - + +
66B GLU* 2.8 41.0 + - - -
130B ARG* 3.5 46.5 + - - +
131B ARG* 6.0 0.2 - - - +
132B PRO* 3.9 17.2 - - + +
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLY* 4.6 2.2 - - - -
207A ASP* 6.5 0.2 - - + -
2B ARG* 4.1 7.9 + - - +
4B GLU 4.5 0.2 - - - +
5B TYR* 3.2 22.1 - - + -
6B CYS* 2.7 40.5 + - - +
21B CYS 3.6 21.6 + - - +
22B GLY* 4.2 1.6 - - - -
23B TRP* 4.3 10.8 - - + -
39B ARG* 1.3 85.4 - - - +
41B ARG* 1.3 64.0 + - - +
42B GLU* 2.9 15.1 + - - +
43B GLY* 3.0 20.2 + - - +
135B ALA* 6.0 0.3 - - - +
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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
------------------------------------------------------------
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