Contacts of the strand formed by residues 32 - 40 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 4.3 16.4 - - + +
25A VAL 3.2 11.9 - - - +
26A PHE* 3.0 35.3 - - + -
27A LEU* 4.8 0.7 - - - -
30A GLY 4.6 4.0 - - - +
31A PHE* 1.3 70.5 - - - +
33A LEU* 1.3 70.8 + - - +
34A ARG* 5.6 0.4 - - + +
2E LYS* 2.3 49.1 + - - +
4E GLY* 4.6 19.7 + - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 3.8 1.0 - - - +
24A THR* 3.5 3.1 - - - -
25A VAL* 2.6 44.8 + - + +
27A LEU* 4.5 13.7 - - + -
31A PHE* 6.4 0.2 - - + -
32A GLN* 1.3 80.8 - - - +
34A ARG* 1.3 58.2 + - - +
35A GLY 4.0 0.4 - - - -
47A LEU* 4.3 16.2 - - + -
49A VAL* 4.3 18.6 - - + -
54A GLN* 4.1 28.5 - - + +
56A VAL* 4.2 23.1 - - + -
63D THR* 4.2 12.3 - - + -
2E LYS* 5.4 7.0 - - - +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.5 27.3 + - + +
23A ALA 3.4 5.8 - - - -
24A THR* 2.6 44.8 + - + +
32A GLN* 5.6 0.4 - - - +
33A LEU* 1.3 74.2 - - - +
35A GLY* 1.3 57.8 + - - +
49A VAL* 3.5 25.9 - - - +
50A GLU* 5.2 1.7 + - - +
65A SER 4.5 4.4 + - - -
67A GLN* 3.4 47.9 + - - +
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.5 13.2 - - - +
23A ALA* 3.0 35.8 + - - +
25A VAL* 5.7 0.9 - - - +
33A LEU 4.0 1.4 + - - -
34A ARG* 1.3 73.3 - - - +
36A ARG* 1.3 61.3 + - - -
37A VAL* 5.8 0.7 - - - +
47A LEU* 4.7 9.3 - - - +
48A ASP 3.4 15.0 - - - -
49A VAL* 4.3 4.5 - - - -
50A GLU 5.7 0.2 - - - -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU 5.6 0.7 - - - +
20A LYS* 2.8 51.2 + - + +
21A ILE 3.7 17.0 - - - +
22A LEU* 3.5 38.2 - - - +
35A GLY* 1.3 75.0 - - - +
37A VAL* 1.3 65.2 + - - +
38A VAL 3.4 0.2 + - - -
47A LEU* 3.4 5.8 - - - -
48A ASP* 2.6 52.4 + - + +
67A GLN* 5.3 1.6 + - - -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.0 12.8 - - + +
16A LEU* 4.2 25.6 + - + -
17A ARG* 3.3 44.7 - - + +
20A LYS* 4.5 8.3 + - - +
21A ILE 5.0 1.1 + - - +
23A ALA* 6.1 2.9 - - + -
35A GLY 5.8 0.4 - - - +
36A ARG* 1.3 73.5 - - - +
38A VAL* 1.3 60.7 + - - +
39A SER 4.0 13.7 - - - +
40A PHE* 4.0 15.3 - - + -
45A VAL* 4.4 7.4 - - + -
46A LEU 3.8 5.4 - - - +
47A LEU* 4.1 14.1 - - + -
64A PHE* 4.4 15.9 - - + -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.2 20.3 + - - +
20A LYS* 5.3 9.0 - - - +
37A VAL* 1.3 74.9 - - - +
39A SER* 1.3 64.9 + - - +
46A LEU* 2.8 33.8 + - + +
47A LEU 4.1 2.9 - - - +
48A ASP* 3.6 36.6 - - + +
53A GLN* 5.7 5.8 - - + +
72D LEU* 4.7 10.1 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 4.5 4.5 - - - +
37A VAL* 3.7 1.4 - - - +
38A VAL* 1.3 82.7 - - - +
40A PHE* 1.3 75.9 + - - +
45A VAL* 3.6 2.4 - - - +
46A LEU* 2.6 37.1 + - - +
8D LEU* 3.8 25.7 - - - +
72D LEU* 4.3 16.3 - - - +
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 3.9 25.8 - - + -
13A LEU* 3.3 52.5 - - + -
14A ASN* 3.7 19.3 - - + -
17A ARG* 4.8 7.2 - - - -
37A VAL* 4.0 12.1 - - + -
39A SER* 1.3 86.3 + - - +
41A ASP* 1.3 68.9 + - - +
44A THR 3.4 14.8 - - - +
45A VAL* 4.1 13.5 - - + -
58A LYS* 4.8 3.1 - - - -
8D LEU* 4.2 8.4 - - - +
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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