Contacts of the strand formed by residues 31 - 39 (chain C) in PDB entry 4JRI
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 LYS 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLU* 3.5 23.2 + - - +
47A LYS* 4.2 27.1 - - - +
48A ASN 4.0 15.9 - - - +
49A THR 4.8 1.5 + - - +
23C SER* 3.7 12.9 + - - -
24C ILE 3.7 4.3 - - - +
25C TYR* 3.4 45.7 + - + +
29C GLY 3.5 3.4 + - - +
30C ILE* 1.3 78.2 - - - +
32C LEU* 1.3 64.9 + - - +
33C GLN* 3.3 36.6 + - + +
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Residues in contact with LEU 32 (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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48A ASN 5.0 6.7 - - - +
49A THR* 5.8 2.2 - - - -
22C VAL 3.8 0.2 - - - +
23C SER* 3.2 4.0 - - - -
24C ILE* 2.7 48.9 + - + +
26C LEU* 4.4 18.2 - - + -
30C ILE* 3.8 21.3 - - + -
31C LYS* 1.3 75.5 - - - +
33C GLN* 1.3 62.4 + - - +
46C LEU* 3.7 13.7 - - + -
52C GLN* 3.6 34.1 - - - +
54C VAL* 3.7 31.6 - - + -
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Residues in contact with GLN 33 (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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19A ARG* 3.5 36.6 - - + +
35A GLN* 3.3 21.6 + - - +
37A GLU* 2.7 26.8 + - - +
47A LYS* 3.5 19.0 - - + +
22C VAL 3.3 6.5 + - - +
23C SER* 3.7 12.0 + - - +
31C LYS* 3.3 27.9 + - + +
32C LEU* 1.3 80.6 - - - +
34C GLY* 1.3 54.7 + - - +
46C LEU* 3.9 7.6 - - - +
48C ASN* 2.4 37.3 + - - +
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Residues in contact with GLY 34 (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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19A ARG* 5.2 6.3 - - - +
35A GLN* 4.6 4.5 - - - -
21C PRO* 4.6 4.7 - - - -
22C VAL* 2.8 40.0 + - - +
33C GLN* 1.3 77.0 - - - +
35C GLN* 1.3 60.9 + - - -
46C LEU* 3.6 8.6 - - - +
47C LYS 3.3 12.1 - - - -
48C ASN* 4.5 2.9 - - - -
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Residues in contact with GLN 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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18A GLU 5.5 3.6 + - - -
66A ARG* 4.9 13.1 - - - +
15C LEU 5.8 0.4 - - - +
16C ARG* 5.7 0.4 - - - +
19C ARG* 2.7 67.2 - - + +
20C VAL 4.9 3.1 - - - +
21C PRO* 3.7 16.7 - - - +
34C GLY* 1.3 72.1 - - - -
36C ILE* 1.3 69.1 + - - +
37C GLU* 3.2 0.4 + - - -
46C LEU* 3.5 4.4 - - - +
47C LYS* 2.8 51.4 + - + +
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Residues in contact with ILE 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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12C LEU* 4.1 21.8 - - + +
15C LEU* 4.4 11.8 + - + -
16C ARG* 3.5 31.0 - - + +
20C VAL 5.0 3.0 + - - -
22C VAL* 3.9 34.5 - - + +
24C ILE* 4.4 8.1 - - + -
34C GLY 3.9 1.4 + - - -
35C GLN* 1.3 80.0 - - - +
37C GLU* 1.3 60.2 + - - +
38C SER 4.1 7.6 - - - +
39C TRP* 3.8 34.3 - - + -
44C ILE* 3.7 23.8 - - + -
45C LEU 4.0 2.2 - - - -
46C LEU* 4.5 1.3 - - + -
62C VAL* 5.3 1.6 - - + -
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Residues in contact with GLU 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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16C ARG* 3.5 18.5 - - - +
35C GLN 3.2 1.0 + - - -
36C ILE* 1.3 74.6 - - - +
38C SER* 1.3 68.2 + - - +
45C LEU* 2.9 29.9 + - + +
47C LYS* 3.8 30.2 + - + +
51C SER* 2.6 34.7 + - - -
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Residues in contact with SER 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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16C ARG* 4.8 0.4 - - - +
36C ILE* 3.8 0.9 - - - +
37C GLU* 1.3 83.2 - - - +
39C TRP* 1.3 87.9 + - - +
44C ILE* 3.5 4.5 - - - +
45C LEU* 2.8 46.6 + - - +
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Residues in contact with TRP 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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9C ASP* 3.1 45.1 + - + +
12C LEU* 3.9 31.8 - - + +
13C ASN* 3.4 40.2 - - - -
16C ARG* 3.7 25.6 - - - -
36C ILE* 3.8 11.9 - - + -
38C SER* 1.3 93.7 + - - +
40C ASP* 1.3 76.4 + - - +
43C VAL* 3.2 18.4 - - - +
44C ILE* 3.8 15.5 - - + +
45C LEU* 4.5 1.3 - - - +
56C LYS* 4.0 3.6 - - - -
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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