Contacts of the strand formed by residues 43 - 49 (chain D) in PDB entry 2NX5
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 PRO 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D TYR* 4.0 15.1 - - + -
36D GLN 3.4 7.2 - - - +
37D GLN* 4.0 14.8 - - + +
41D GLU 3.9 0.2 - - - -
42D ALA* 1.3 90.1 - - + +
44D THR* 1.3 61.0 + - - +
89D LEU* 3.6 32.5 - - + -
43E LEU* 3.9 16.6 - - + -
91E PHE* 4.1 8.5 - - + -
106E GLN 5.4 0.7 - - - +
108E PHE* 3.7 39.6 + - + +
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D TYR* 3.3 8.3 - - - -
36D GLN* 2.8 52.7 + - - +
38D HIS* 6.5 1.6 - - + -
42D ALA* 4.0 11.7 - - + +
43D PRO* 1.3 77.2 - - - +
45D PHE* 1.3 65.9 + - - +
46D LEU* 4.2 2.1 - - - +
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Residues in contact with PHE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 6.0 2.9 - - - -
33D PHE* 3.5 24.5 - + - -
34D TRP 4.4 2.2 - - - -
35D TYR* 3.7 12.3 - + + -
44D THR* 1.3 77.3 + - - +
46D LEU* 1.3 69.4 + - - +
47D SER* 3.4 25.6 - - - -
48D TYR* 3.5 21.3 - - + -
57D LYS* 3.7 21.5 - - - -
100E ASN 5.7 0.9 - - - -
105E PRO* 3.4 44.6 - - + -
106E GLN 5.3 1.1 - - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TRP* 3.0 18.0 + - + +
35D TYR* 4.0 2.7 - - - +
36D GLN* 3.7 44.6 - - + +
44D THR* 4.8 3.4 - - - +
45D PHE* 1.3 82.4 - - - +
47D SER* 1.3 63.3 + - - +
57D LYS* 3.0 29.9 + - - +
62D PHE* 3.9 31.7 - - + +
75D LEU* 3.9 29.6 - - + -
88D TYR* 3.9 4.3 - - + -
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE* 3.4 5.7 - - - -
34D TRP* 3.0 36.6 + - - +
45D PHE* 3.4 15.0 - - - -
46D LEU* 1.3 82.9 - - - +
48D TYR* 1.3 59.7 + - - +
49D ASN* 3.3 11.3 + - - -
55D GLU* 4.3 11.4 - - - -
57D LYS* 4.2 3.8 - - - +
64D SER* 2.6 34.2 + - - -
75D LEU* 4.8 1.5 - - - +
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Residues in contact with TYR 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 4.4 6.5 - - - +
154A GLU* 3.8 23.2 + - + -
155A GLN* 5.0 0.7 + - - -
158A ALA* 4.6 5.7 - - - +
30D ASN* 4.7 1.8 + - - -
31D GLY* 4.2 11.9 - - - -
32D LEU 3.5 4.5 - - - -
33D PHE* 3.6 34.1 - + + -
45D PHE* 3.5 10.6 - - + -
47D SER* 1.3 73.4 - - - +
49D ASN* 1.3 67.1 + - - +
50D VAL* 3.3 44.7 + - + +
55D GLU* 5.3 5.0 - - - +
57D LYS* 5.2 0.4 - - - +
99E SER* 3.3 22.8 + - - -
100E ASN* 3.4 35.0 + - + +
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Residues in contact with ASN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLY* 3.5 0.9 - - - -
32D LEU* 2.6 71.0 + - + +
34D TRP* 3.6 4.2 - - - -
47D SER* 3.3 22.9 + - - -
48D TYR* 1.3 78.6 - - - +
50D VAL* 1.3 60.7 + - - +
51D LEU 5.1 1.8 - - - +
55D GLU* 4.7 6.1 - - - +
64D SER* 2.9 32.2 - - - +
65D PHE 5.2 1.6 - - - -
66D LEU* 3.6 27.7 - - + +
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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