Contacts of the strand formed by residues 49 - 54 (chain A) in PDB entry 3NA1
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 ILE 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.4 8.7 - - + -
13A PRO* 3.8 18.6 - - + +
43A PHE* 4.5 0.4 - - - -
46A TYR 4.2 6.1 - - - +
47A GLY 3.1 1.8 + - - +
48A PRO* 1.3 84.3 - - + +
50A TYR* 1.3 69.6 + - - +
60A VAL* 3.8 23.6 - - + -
61A TYR 3.4 13.5 - - - +
62A VAL* 4.6 8.3 - - + -
365A LEU* 4.1 32.5 - - + +
366A ARG* 3.9 25.1 - - + -
368A TYR* 3.9 26.5 - - + -
370A ILE* 4.3 4.7 - - + -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.6 8.1 - - - -
13A PRO 3.3 15.3 - - - +
15A PRO* 5.2 0.2 - - + -
39A HIS* 3.5 26.2 - - - +
42A ASN* 3.2 48.9 + - + +
43A PHE* 3.5 40.3 - + - -
46A TYR* 3.8 25.8 - + + -
47A GLY 4.7 1.1 - - - -
49A ILE* 1.3 75.6 - - - +
51A ARG* 1.3 67.9 + - - +
52A GLU* 4.1 7.6 + - + -
60A VAL* 3.4 4.7 - - - +
61A TYR* 2.7 66.0 + + + +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.5 37.0 + - + -
10A ASN* 3.0 32.2 + - - +
12A ILE* 3.1 24.7 + - + +
13A PRO 3.0 5.9 + - - -
14A SER* 2.8 53.1 + - - +
15A PRO* 3.6 1.4 - - - +
16A GLY 4.9 3.0 + - - -
17A ASP* 3.1 29.7 + - - -
50A TYR* 1.3 77.3 - - - +
52A GLU* 1.3 63.5 - - - +
58A GLU* 3.0 27.0 + - - +
59A SER 3.2 12.1 - - - +
60A VAL* 4.1 10.5 - - + -
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Residues in contact with GLU 52 (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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14A SER* 5.0 0.9 - - - -
15A PRO* 3.5 30.3 - - + +
16A GLY 5.6 0.2 - - - -
22A ASN* 4.3 7.4 - - - +
38A HIS* 3.0 38.7 + - - -
39A HIS* 5.8 0.3 - - - -
42A ASN* 3.6 10.2 + - - +
50A TYR* 4.1 8.3 + - + -
51A ARG* 1.3 77.3 - - - +
53A LYS* 1.3 72.7 + - - +
54A LEU* 3.7 26.0 + - + +
57A VAL 3.8 0.9 - - - +
58A GLU* 3.6 5.4 - - - +
59A SER 3.0 25.8 + - - +
61A TYR* 4.0 21.6 + - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 4.9 3.4 + - - +
17A ASP* 3.9 21.1 + - - +
19A GLY* 3.4 11.4 - - - +
22A ASN* 3.0 36.8 + - - +
52A GLU* 1.3 72.1 - - - +
54A LEU* 1.3 62.1 + - - +
55A GLY 3.7 19.6 + - - +
56A ASN* 3.8 24.2 + - - +
57A VAL 3.3 14.1 - - - +
58A GLU* 3.8 28.5 + - + +
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Residues in contact with LEU 54 (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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19A GLY 3.9 0.4 - - - -
22A ASN 4.0 5.6 - - - +
23A LEU* 4.0 30.3 - - + +
26A PHE* 4.3 19.7 - - + -
35A VAL* 6.0 4.5 - - + -
38A HIS* 5.0 4.5 - - + +
39A HIS* 6.4 0.2 - - - +
52A GLU* 3.7 33.1 + - + +
53A LYS* 1.3 77.9 - - - +
55A GLY* 1.3 63.5 + - - +
56A ASN 3.3 0.2 + - - -
57A VAL* 2.8 26.8 + - - +
61A TYR* 4.4 13.7 - - - +
210A ASN* 3.5 40.1 - - - +
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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