Contacts of the strand formed by residues 32 - 40 (chain J) in PDB entry 4NL3
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 GLN 32 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET 3.7 11.6 + - - -
2C LYS 4.0 2.9 + - - +
3C GLN* 3.4 27.1 - - + +
4C GLY* 4.7 4.2 - - - +
5C GLY 4.9 6.1 - - - +
24J THR* 3.9 19.1 - - + +
25J VAL 3.2 10.5 - - - +
26J PHE* 3.7 33.5 - - + -
30J GLY 4.6 4.8 + - - -
31J PHE* 1.3 77.2 - - - +
33J LEU* 1.3 70.0 + - - +
34J ARG* 5.7 1.9 - - + +
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Residues in contact with LEU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B THR* 4.9 5.4 - - + +
1C MET* 3.8 24.2 - - - +
23J ALA 3.6 1.2 - - - +
24J THR* 3.4 2.3 - - - -
25J VAL* 2.5 51.1 + - + +
27J LEU* 3.8 39.7 - - + -
31J PHE* 5.5 1.3 - - + -
32J GLN* 1.3 82.4 - - - +
34J ARG* 1.3 60.7 + - - +
47J LEU* 4.5 9.2 - - + -
49J VAL* 3.8 26.9 - - + -
54J GLN* 3.9 25.8 - - + +
56J VAL* 4.8 6.7 - - + -
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Residues in contact with ARG 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 5.2 0.8 - - - +
22J LEU* 3.2 55.5 + - + +
23J ALA* 3.4 3.6 - - - +
24J THR* 2.5 52.3 + - + +
32J GLN* 5.6 2.4 - - + +
33J LEU* 1.3 72.5 - - - +
35J GLY* 1.3 57.7 + - - +
49J VAL* 3.4 26.2 - - - +
50J GLU* 4.7 4.5 + - - +
65J SER 4.9 1.4 + - - -
66J PRO 6.0 0.2 - - - -
67J GLN* 3.8 18.8 + - - +
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Residues in contact with GLY 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J ILE 4.0 0.5 - - - +
22J LEU* 3.4 9.7 - - - +
23J ALA* 3.0 34.7 + - - +
25J VAL* 5.6 1.7 - - - +
33J LEU 4.0 1.4 + - - -
34J ARG* 1.3 74.6 - - - +
36J ARG* 1.3 65.9 + - - -
37J VAL* 4.4 0.9 + - - +
47J LEU* 4.6 8.8 - - - +
48J ASP 3.2 15.0 - - - -
49J VAL* 4.4 4.2 - - - +
50J GLU 5.4 0.4 - - - -
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Residues in contact with ARG 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LYS* 3.4 32.6 + - + +
21J ILE 3.7 17.3 - - - +
22J LEU* 4.0 21.0 - - + +
35J GLY* 1.3 77.1 - - - -
37J VAL* 1.3 65.7 + - - +
38J VAL* 3.4 0.6 + - + -
47J LEU* 3.5 4.7 - - - -
48J ASP* 2.6 53.9 + - + +
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Residues in contact with VAL 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LEU* 3.9 13.0 - - + +
16J LEU* 4.1 23.0 + - + +
17J ARG* 3.4 46.6 - - + +
20J LYS* 5.8 0.9 - - - +
21J ILE 4.6 4.1 + - - +
23J ALA* 5.9 3.4 - - + -
35J GLY 5.7 0.7 - - - +
36J ARG* 1.3 74.9 - - - +
38J VAL* 1.3 61.3 + - - +
39J SER 4.0 19.3 - - - +
40J PHE* 4.8 4.3 - - + -
45J VAL* 4.2 11.2 - - + -
46J LEU 3.8 3.1 - - - -
47J LEU* 4.0 13.5 - - + -
64J PHE* 4.5 17.5 - - + -
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Residues in contact with VAL 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.6 36.1 - - + -
17J ARG* 3.2 22.3 + - - +
36J ARG 3.4 0.4 + - - -
37J VAL* 1.3 75.0 - - - +
39J SER* 1.3 65.0 + - - +
46J LEU* 2.9 26.4 + - + +
47J LEU 4.3 2.5 - - - -
48J ASP* 3.7 34.1 - - + +
53J GLN* 5.6 4.3 - - + +
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Residues in contact with SER 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.7 27.1 - - - +
72B LEU* 5.2 4.3 - - - -
17J ARG* 4.3 5.3 - - - +
37J VAL* 3.7 2.2 - - - +
38J VAL* 1.3 87.9 - - - +
40J PHE* 1.3 78.3 + - - +
45J VAL* 3.6 2.9 - - - +
46J LEU* 2.7 33.6 + - - +
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Residues in contact with PHE 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.3 8.4 - - - +
10J ASP* 3.7 38.6 - - + -
13J LEU* 3.5 35.2 - - + -
14J ASN* 3.7 33.2 - - + -
17J ARG* 4.6 7.0 - - - -
37J VAL* 4.8 3.6 - - + -
39J SER* 1.3 91.9 + - - +
41J ASP* 1.3 67.2 + - - +
44J THR 3.5 14.6 - - - +
45J VAL* 4.1 14.4 - - + -
58J LYS* 4.4 2.2 - - - -
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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