Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 1CN4
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 VAL 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.4 15.7 - - + -
27A LEU 3.8 1.2 - - - +
28A CYS* 2.9 21.5 - - - +
29A PHE* 3.1 43.9 + - + +
31A GLU* 5.9 1.3 - - + +
35A ASP* 6.0 0.7 - - - +
36A LEU* 1.3 78.3 - - - +
38A CYS* 1.3 74.8 + - - +
39A PHE* 5.1 0.7 - - + -
82A TRP* 4.0 18.6 - - + -
83A CYS 3.3 12.6 - - - +
84A SER* 4.5 11.2 - - - +
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Residues in contact with CYS 38 (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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26A LEU* 4.0 10.5 - - + -
27A LEU 3.5 4.5 - - - -
28A CYS* 2.0 46.4 - - - -
36A LEU* 4.2 13.2 - - - -
37A VAL* 1.3 78.0 - - - +
39A PHE* 1.3 62.4 + - - +
40A TRP* 4.8 1.4 - - - -
55A PHE* 3.8 26.2 - - + -
81A PHE 4.3 0.2 - - - -
82A TRP* 3.0 5.0 - - - +
83A CYS* 3.0 30.8 + - - +
85A LEU* 5.9 1.3 - - - -
98A LEU* 3.8 9.9 - - - -
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Residues in contact with PHE 39 (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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11A PHE* 4.8 5.4 - + + -
15A ALA* 3.5 32.8 - - + -
18A LEU* 4.4 4.0 - - + -
19A ALA* 4.7 1.1 - - + -
26A LEU* 3.0 14.4 - - - +
27A LEU* 2.9 71.4 + - + +
29A PHE* 4.4 21.1 - + - -
37A VAL* 5.1 0.9 - - + -
38A CYS* 1.3 78.1 - - - +
40A TRP* 1.3 70.9 + - - +
41A GLU* 3.9 15.7 - - + -
80A ARG* 3.4 34.8 - - + -
81A PHE 2.9 20.2 - - - +
82A TRP* 3.9 10.5 - - + -
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Residues in contact with TRP 40 (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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23A PRO 4.1 5.2 - - - +
25A GLU 4.1 9.4 - - - +
26A LEU* 3.3 26.0 - - + -
27A LEU* 5.9 2.2 - - - -
38A CYS 4.8 0.7 - - - -
39A PHE* 1.3 87.0 - - - +
41A GLU* 1.3 68.4 + - - +
42A GLU* 3.8 18.5 + - - -
53A TYR* 4.5 13.9 - + - -
55A PHE* 4.3 18.6 - + - -
69A LEU* 4.1 18.6 - - + -
79A VAL 3.9 1.4 - - - +
80A ARG* 3.9 0.5 - - - -
81A PHE* 3.2 71.0 + + + -
100A VAL* 4.0 26.7 - - + -
108A ARG* 4.8 0.6 - - - +
109A TYR* 3.4 40.2 - + + +
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Residues in contact with GLU 41 (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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19A ALA* 3.7 25.1 - - + +
23A PRO* 4.6 23.3 + - + +
24A GLU* 4.2 9.0 - - - +
39A PHE* 3.9 8.6 - - + -
40A TRP* 1.3 82.7 - - - +
42A GLU* 1.3 66.8 + - - +
74A THR* 4.2 16.6 + - + +
76A ARG* 5.5 5.4 - - - +
78A ALA* 4.5 10.0 - - + +
79A VAL 3.5 6.7 - - - +
80A ARG* 2.6 43.1 + - + +
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Residues in contact with GLU 42 (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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24A GLU* 4.6 5.2 - - - +
40A TRP* 3.8 12.2 + - + +
41A GLU* 1.3 78.2 - - - +
43A ALA* 1.3 67.1 + - - +
44A ALA* 3.8 5.0 + - + +
48A VAL* 4.4 8.1 - - - +
53A TYR* 2.5 34.1 + - - -
78A ALA* 3.7 5.6 - - - +
79A VAL* 3.1 32.3 + - + +
81A PHE* 3.8 4.9 - - + -
108A ARG* 2.3 37.4 + - - -
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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