Contacts of the strand formed by residues 39 - 45 (chain A) in PDB entry 1N6U
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 TYR 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TRP* 3.0 41.3 - + + -
29A LEU* 3.1 35.7 + - + +
31A ASN* 5.3 3.3 + - - -
36A PRO* 4.3 23.0 + - + +
37A THR* 3.3 20.1 + - - -
38A HIS* 1.3 78.1 - - - +
40A THR* 1.3 58.4 + - - +
58A CYS 3.9 1.3 - - - -
59A ALA 2.8 1.7 - - - -
60A ASN* 2.4 28.5 + - - -
61A THR* 2.8 14.7 + - - +
63A ARG 3.0 15.7 - - - -
64A SER* 4.7 1.8 - - - -
83A LEU* 3.8 7.2 - - + -
85A GLY* 3.6 9.0 - - - -
86A PHE* 4.0 2.2 - - - +
93A PHE* 3.4 28.9 - + - -
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Residues in contact with THR 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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39A TYR* 1.3 71.2 - - - +
41A LEU* 1.3 60.5 + - - +
42A LEU* 3.1 30.0 + - + +
54A VAL* 3.4 21.5 - - + -
58A CYS 3.1 4.3 - - - -
59A ALA* 3.3 2.0 - - - -
60A ASN* 2.7 24.8 + - - -
83A LEU* 3.8 2.5 - - - -
84A GLU 2.8 32.0 + - - -
86A PHE* 2.8 34.6 - - + -
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Residues in contact with LEU 41 (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 PHE* 5.2 0.4 - - + -
25A LEU* 2.9 54.1 - - + +
26A SER 4.9 1.1 - - - +
27A TRP* 3.1 35.0 - - + -
40A THR* 1.3 69.8 - - - +
42A LEU* 1.3 60.0 + - - +
43A TYR* 5.4 1.6 - - + -
53A LYS 3.4 1.2 - - - +
54A VAL* 3.7 0.9 - - - -
55A VAL* 3.2 33.9 + - + +
58A CYS* 2.6 23.7 + - + -
66A CYS* 3.3 26.9 - - + -
68A LEU* 4.8 0.2 - - + -
81A THR* 4.6 5.6 - - + -
83A LEU* 3.8 18.3 - - + +
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Residues in contact with LEU 42 (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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40A THR* 3.3 12.8 - - + +
41A LEU* 1.3 73.4 - - - +
43A TYR* 1.3 56.9 + - - +
52A LEU* 2.9 18.8 - - + -
53A LYS 3.3 6.1 - - - +
54A VAL* 3.0 44.4 - - + -
81A THR* 2.9 8.2 - - - +
82A VAL* 2.6 52.0 + - + +
84A GLU* 3.1 51.4 - - + +
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Residues in contact with TYR 43 (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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25A LEU* 5.0 1.1 - - + -
41A LEU* 4.8 3.1 - - + -
42A LEU* 1.3 72.5 - - - +
44A THR* 1.3 62.6 + - - +
51A ASP 3.5 3.1 - - - +
52A LEU* 2.8 10.4 - - - +
53A LYS* 2.7 58.9 + - + +
55A VAL* 3.2 37.5 - - + -
68A LEU* 6.0 0.9 - - + -
71A GLU* 3.3 37.0 + - + +
72A TRP* 3.1 23.3 - + + +
79A TYR* 3.2 27.6 - + - -
80A VAL 3.7 0.4 - - - -
81A THR* 3.1 26.7 - - + -
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Residues in contact with THR 44 (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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43A TYR* 1.3 76.2 - - - +
45A ILE* 1.3 57.3 + - - +
48A LYS 2.4 29.8 + - - -
49A PRO* 3.4 11.6 - - + +
51A ASP* 3.1 22.1 + - - +
52A LEU* 3.3 29.4 - - + -
79A TYR* 3.1 15.7 - - - -
80A VAL* 2.5 63.2 + - + +
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Residues in contact with ILE 45 (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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44A THR* 1.3 80.8 + - - +
46A MET* 1.3 56.3 + - - +
47A SER* 4.5 3.6 - - - +
48A LYS* 2.5 76.1 + - + +
49A PRO 3.0 0.5 - - - -
51A ASP* 5.4 4.3 - - + +
74A SER* 3.5 37.5 - - - +
77A GLU* 3.6 21.3 - - + -
78A ALA 3.9 1.1 - - - -
79A TYR* 3.7 22.9 - - + +
80A VAL* 3.2 3.8 - - - -
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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