Contacts of the strand formed by residues 34 - 39 (chain C) in PDB entry 4IJ3
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 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.5 6.5 - - + -
22C CYS* 4.3 4.5 - - - -
24C VAL* 4.2 12.3 - - + -
27C PHE* 4.6 3.1 - - + -
29C LEU* 4.0 13.7 - - + -
33C GLY* 1.3 80.6 - - - +
35C ASN* 1.3 77.6 + - - +
36C TRP* 4.5 4.2 - - - +
50C MET* 3.3 1.8 - - - +
51C ILE* 3.0 34.6 + - + +
78C VAL* 3.8 39.9 - - + -
95C CYS* 3.9 19.3 - - + -
96C ALA 3.8 8.7 - - - +
97C SER* 5.4 0.7 - - - -
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Residues in contact with ASN 35 (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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33C GLY 5.4 1.0 - - - -
34C VAL* 1.3 82.6 - - - +
36C TRP* 1.3 64.4 + - - +
37C VAL* 5.1 1.1 - - + -
47C TRP* 2.7 27.7 + - + +
49C GLY 3.3 4.3 - - - -
50C MET* 3.1 31.3 - - - +
95C CYS* 3.1 7.4 - - - -
96C ALA* 2.8 37.7 + - + +
98C ASP* 4.5 13.5 - - - +
105C PHE* 3.2 33.0 - - + -
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Residues in contact with TRP 36 (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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6C GLN* 4.3 5.6 - - + -
20C ILE* 3.8 37.7 - - + -
22C CYS* 3.6 32.5 - - + -
34C VAL* 4.5 2.6 - - - +
35C ASN* 1.3 78.7 + - - +
37C VAL* 1.3 65.5 + - - +
47C TRP* 3.7 2.1 - - - -
48C LEU* 2.8 45.1 + - + +
49C GLY 2.8 10.9 + - - +
69C ILE* 3.6 44.3 - - + +
78C VAL* 3.7 15.4 - - + +
80C LEU* 3.5 40.4 - - + +
93C TYR* 4.8 2.2 - + + -
94C PHE 3.1 31.0 - - - -
95C CYS* 3.9 11.2 - - + -
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Residues in contact with VAL 37 (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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98B PHE* 4.3 8.1 - - + -
35C ASN* 5.1 2.2 - - + -
36C TRP* 1.3 82.1 - - - +
38C ARG* 1.3 60.6 + - - +
45C LEU* 4.0 15.3 - - + -
46C GLU 3.4 26.9 - - - +
47C TRP* 4.1 19.3 - - + -
48C LEU* 4.4 2.2 - - - -
94C PHE* 2.6 49.3 + - + +
96C ALA* 5.3 4.3 - - + -
105C PHE* 4.5 7.6 - - + -
108C TRP* 3.8 36.3 - - + -
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Residues in contact with ARG 38 (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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37C VAL* 1.3 76.7 - - - +
39C GLN* 1.3 64.7 + - - +
40C SER* 5.2 1.3 - - - +
44C GLY 3.8 0.2 - - - +
45C LEU* 3.8 1.0 - - - -
46C GLU* 2.7 63.7 + - + +
48C LEU* 3.6 22.6 - - + +
60C LYS* 6.0 0.2 - - - +
63C LEU* 4.5 16.7 - - - +
66C ARG* 4.8 0.4 - - - +
82C MET* 4.6 6.1 - - - -
88C ASP* 4.5 10.5 + - - -
89C ASP* 2.8 34.9 + - - +
91C ALA* 4.4 7.2 - - + -
92C ARG 3.1 9.6 - - - +
93C TYR* 2.8 61.2 + - + +
94C PHE* 4.9 0.4 - - - -
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Residues in contact with GLN 39 (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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38B GLN* 2.8 40.6 + - - -
87B TYR* 3.4 8.9 + - - -
38C ARG* 1.3 76.2 - - - +
40C SER* 1.3 69.2 + - - +
41C PRO* 3.3 2.5 - - + +
42C GLY 5.8 1.1 - - - +
43C LYS 3.2 27.4 + - - +
44C GLY 3.5 9.4 - - - +
45C LEU* 3.3 22.6 - - + +
91C ALA* 3.3 2.9 - - - -
92C ARG* 2.8 36.9 + - + +
94C PHE* 3.9 14.4 - - + -
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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