Contacts of the strand formed by residues 32 - 40 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C THR* 4.1 17.6 - - + +
25C VAL 3.6 6.7 - - - +
26C PHE* 3.7 38.4 - - + -
27C LEU* 4.8 1.1 - - - -
30C GLY 3.6 11.9 + - - +
31C PHE* 1.3 82.8 - - - +
33C LEU* 1.3 73.0 + - - +
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Residues in contact with LEU 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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23C ALA 3.9 0.5 - - - +
24C THR* 3.6 3.7 - - - +
25C VAL* 2.7 43.5 + - + +
27C LEU* 4.4 15.3 - - + -
32C GLN* 1.3 80.1 - - - +
34C ARG* 1.3 59.7 + - - +
35C GLY 4.0 1.0 + - - -
47C LEU* 4.2 11.7 - - + -
49C VAL* 4.1 21.3 - - + -
54C GLN* 3.9 30.7 - - + +
56C VAL* 3.8 29.2 - - + -
63F THR* 4.3 11.0 - - + +
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Residues in contact with ARG 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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22C LEU* 3.5 30.5 - - + -
23C ALA 3.6 5.8 - - - +
24C THR* 4.3 17.4 + - + +
33C LEU* 1.3 72.1 - - - +
35C GLY* 1.3 57.8 + - - +
49C VAL* 3.3 25.4 - - - +
50C GLU* 4.0 17.8 + - - +
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Residues in contact with GLY 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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22C LEU* 4.4 5.2 - - - -
23C ALA* 3.0 35.6 + - - +
25C VAL* 5.5 3.1 - - - +
33C LEU 4.0 1.8 + - - -
34C ARG* 1.3 76.4 - - - +
36C ARG* 1.3 64.8 + - - +
37C VAL* 5.8 0.3 - - - +
47C LEU* 5.0 6.9 - - - +
48C ASP 3.3 14.1 - - - -
49C VAL* 4.3 4.5 - - - +
50C GLU* 5.0 3.1 - - - -
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Residues in contact with ARG 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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20C LYS* 3.2 37.6 + - - +
21C ILE 3.5 16.6 - - - +
22C LEU* 3.8 33.7 - - + +
23C ALA* 6.0 0.2 - - - -
35C GLY* 1.3 78.0 - - - +
37C VAL* 1.3 66.8 + - - +
38C VAL* 6.0 0.2 - - + -
47C LEU* 3.3 5.9 - - - +
48C ASP* 2.7 51.6 + - + +
67C GLN* 5.2 2.0 + - - -
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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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13C LEU* 3.8 20.2 - - + +
16C LEU* 4.0 29.4 + - + +
17C ARG* 3.5 34.7 - - + +
20C LYS* 6.0 0.5 - - - -
21C ILE 4.7 3.2 + - - +
23C ALA* 5.8 4.0 - - + -
35C GLY 5.8 0.2 - - - +
36C ARG* 1.3 74.2 - - - +
38C VAL* 1.3 62.7 + - - +
39C SER 4.0 8.3 - - - +
40C PHE* 3.9 18.8 - - + -
45C VAL* 4.4 6.7 - - + -
46C LEU 3.8 4.9 - - - +
47C LEU* 4.1 11.2 - - + -
64C PHE* 4.4 13.2 - - + -
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Residues in contact with VAL 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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17C ARG* 3.3 21.7 + - - +
36C ARG 4.9 0.2 - - - -
37C VAL* 1.3 73.5 - - - +
39C SER* 1.3 67.4 + - - +
46C LEU* 2.8 32.8 + - + +
47C LEU 4.0 4.0 - - - +
48C ASP* 3.6 37.5 - - + +
53C GLN* 5.7 5.8 - - + +
72F LEU* 4.9 18.2 - - + -
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Residues in contact with SER 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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17C ARG* 4.4 5.6 - - - +
37C VAL* 3.7 1.0 - - - +
38C VAL* 1.3 84.5 - - - +
40C PHE* 1.3 72.7 + - - +
45C VAL* 3.7 2.4 - - - +
46C LEU* 2.8 36.5 + - - +
8F LEU* 3.2 28.7 - - - +
72F LEU* 5.8 0.9 - - - +
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Residues in contact with PHE 40 (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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10C ASP* 3.7 27.4 - - + -
13C LEU* 3.3 45.3 - - + -
14C ASN* 3.5 27.8 - - + -
17C ARG* 4.4 11.4 - - - -
37C VAL* 3.9 10.5 - - + -
39C SER* 1.3 85.4 + - - +
41C ASP* 1.3 66.8 + - - +
44C THR 3.6 14.4 - - - +
45C VAL* 4.2 14.8 - - + -
58C LYS* 4.9 3.4 - - - -
8F LEU* 4.3 8.6 - - - +
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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