Contacts of the strand formed by residues 38 - 46 (chain X) in PDB entry 2CL7
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 38 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35X THR* 5.5 3.1 - - + -
36X ILE 5.3 1.1 - - - +
37X GLU* 1.3 77.0 - - - +
39X SER* 1.3 69.4 + - - +
40X TYR* 4.0 21.0 - - + +
55X ILE 3.8 0.2 - - - +
56X LEU* 4.5 2.8 - - - +
57X ASP* 3.0 37.6 + - - +
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Residues in contact with SER 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ASP* 1.3 81.9 + - - +
40X TYR* 1.3 64.9 + - - +
41X ARG* 5.8 2.8 - - - -
54X ASP* 4.5 10.2 + - - -
55X ILE 2.9 15.7 - - - -
56X LEU* 4.1 15.2 - - - +
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Residues in contact with TYR 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X SER* 5.5 0.9 - - - -
20X THR* 3.7 21.1 - - + -
21X ILE* 3.5 35.7 - - + +
24X ILE* 3.2 47.8 - - + -
25X GLN* 4.3 14.4 - - - -
38X ASP* 4.0 32.8 + - + +
39X SER* 1.3 79.8 - - - +
41X ARG* 1.3 64.6 + - - +
53X LEU 3.8 0.3 - - - +
55X ILE* 2.8 35.5 + - + +
57X ASP* 4.2 16.0 + - + -
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Residues in contact with ARG 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X GLU* 3.1 38.3 + - - -
24X ILE* 4.2 5.8 - - - +
39X SER* 5.8 2.9 - - - +
40X TYR* 1.3 79.0 - - - +
42X LYS* 1.3 61.3 + - - +
52X LEU* 3.3 22.8 - - + +
53X LEU 3.1 11.4 - - - +
54X ASP* 2.9 34.7 + - - +
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Residues in contact with LYS 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU 3.7 9.7 + - - +
24X ILE* 2.9 51.6 + - + +
26X ASN* 3.7 18.0 + - - +
41X ARG* 1.3 74.9 - - - +
43X GLN* 1.3 72.4 + - - +
44X VAL* 3.7 22.1 + - + +
52X LEU* 4.3 5.3 - - - +
53X LEU* 2.9 37.8 + - + +
149X ARG* 5.8 0.2 - - - +
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Residues in contact with GLN 43 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1X MET* 3.5 24.2 - - - +
42X LYS* 1.3 79.9 - - - +
44X VAL* 1.3 64.5 + - - +
50X THR* 3.9 20.2 - - + +
51X CYS 3.4 16.4 - - - +
52X LEU* 3.5 17.4 - - + +
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Residues in contact with VAL 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU* 5.9 4.0 - - + +
42X LYS* 4.1 29.8 - - + +
43X GLN* 1.3 82.3 - - - +
45X VAL* 1.3 64.5 + - - +
46X ILE* 4.1 13.0 - - + -
50X THR* 3.9 3.5 - - - +
51X CYS* 3.1 32.4 + - - +
53X LEU* 3.8 33.9 - - + -
157X TYR* 3.6 21.1 - - + +
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Residues in contact with VAL 45 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44X VAL* 1.3 79.6 - - - +
46X ILE* 1.3 63.0 + - - +
47X ASP 4.4 0.6 + - - +
48X GLY* 4.0 26.7 - - - +
49X GLU 3.6 7.0 - - - +
50X THR* 4.5 15.5 - - + +
157X TYR* 3.6 19.3 + - - -
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Residues in contact with ILE 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X VAL* 4.1 6.1 - - + -
45X VAL* 1.3 78.7 - - - +
47X ASP* 1.3 82.7 + - - +
48X GLY 3.2 0.2 - - - -
49X GLU* 3.0 19.6 + - - +
51X CYS* 3.9 19.1 - - - -
53X LEU* 4.2 6.3 - - + -
157X TYR* 3.8 50.3 - - + +
160X VAL* 3.7 34.3 - - + -
161X ARG* 4.5 3.6 - - - +
164X ARG* 3.0 32.9 + - - +
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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