Contacts of the strand formed by residues 29 - 37 (chain T) 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 PHE 29 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158Q ALA 5.2 0.7 - - - +
163Q LEU* 4.2 7.8 + - - +
166Q GLU* 4.3 4.8 + - - +
24T TYR* 3.6 34.1 - + + -
26T THR* 3.3 26.7 - - + +
27T SER 3.1 3.4 + - - -
28T GLY* 1.3 77.1 - - - +
30T ASN* 1.3 63.5 + - - +
31T GLY* 3.3 40.2 - - - -
32T LEU* 3.7 8.7 - - + -
49T ASN 3.9 6.1 - - - -
50T VAL* 4.3 4.0 - - + -
66T LEU* 4.0 8.7 - - + -
68T ARG* 3.5 59.7 + - + +
92T VAL* 3.7 13.5 - - + -
93T GLN 3.9 2.5 - - - -
94T ALA* 4.4 1.1 - - - -
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Residues in contact with ASN 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Q GLN 5.4 1.7 + - - +
158Q ALA* 4.3 21.8 + - - +
159Q TYR* 4.7 4.9 - - - +
163Q LEU* 3.4 28.4 - - - +
4S PRO* 4.4 11.2 - - - +
28T GLY 3.1 0.4 + - - +
29T PHE* 1.3 74.8 + - - +
31T GLY* 1.3 55.4 + - - +
48T TYR* 3.5 4.5 + - - -
50T VAL* 4.1 7.9 - - - -
93T GLN* 2.7 35.9 + - + +
102T TYR* 3.6 28.6 - - + -
99U SER* 3.4 24.1 + - - -
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Residues in contact with GLY 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T PHE* 3.3 25.1 - - - -
30T ASN* 1.3 75.5 - - - +
32T LEU* 1.3 57.5 + - - -
33T PHE* 5.2 0.4 - - - -
48T TYR* 3.6 18.4 - - - -
49T ASN 3.3 11.2 - - - -
50T VAL* 3.8 4.3 - - - +
91T ALA 4.2 0.2 - - - +
92T VAL* 3.6 0.9 - - - +
93T GLN* 3.0 28.6 + - - -
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Residues in contact with LEU 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T CYS* 4.5 0.2 - - - -
24T TYR* 3.6 35.7 - - + -
29T PHE* 3.7 10.1 - - + -
31T GLY* 1.3 74.0 - - - +
33T PHE* 1.3 67.7 + - - +
34T TRP* 3.5 35.4 - - + +
48T TYR* 3.6 2.4 - - - -
49T ASN* 2.7 48.0 + - + +
66T LEU* 4.7 4.0 - - + -
73T SER* 3.6 17.9 - - - +
90T CYS* 3.7 20.9 - - - -
91T ALA 3.3 10.1 - - - +
92T VAL* 3.8 5.8 - - + -
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Residues in contact with PHE 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T LEU* 1.3 76.8 - - - +
34T TRP* 1.3 61.6 + - - +
35T TYR* 3.6 27.8 - - + -
45T PHE* 3.5 34.1 - + - -
47T SER 3.4 2.7 - - - -
48T TYR* 3.3 27.8 - + + -
89T LEU 3.6 0.7 - - - +
90T CYS* 3.6 3.6 - - - -
91T ALA* 2.6 45.8 + - + +
93T GLN* 3.4 26.9 - - + -
104T PRO* 4.7 11.2 - - + -
99U SER 3.3 20.9 - - - -
101U GLN* 3.1 35.2 - - - -
105U PRO* 3.8 3.8 - - + -
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Residues in contact with TRP 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLN* 4.3 2.0 - - - -
20T ILE* 3.7 38.1 - - + -
21T ASN 4.2 0.7 - - - -
22T CYS* 3.7 22.9 - - + -
32T LEU* 3.5 19.6 - - + +
33T PHE* 1.3 73.9 - - - +
35T TYR* 1.3 69.0 + - - +
45T PHE* 4.4 0.7 - - - -
46T LEU* 3.0 31.5 + - + +
47T SER* 2.9 24.1 + - - +
49T ASN* 4.0 1.1 - - - -
64T SER* 3.4 24.4 + - - -
73T SER* 3.4 17.6 + - - -
74T TYR* 4.1 6.8 - - - -
75T LEU* 3.6 31.9 - - + -
88T TYR* 3.9 23.8 - - + -
89T LEU 3.3 21.5 - - - -
90T CYS* 3.9 17.5 - - + -
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Residues in contact with TYR 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T PHE* 3.6 36.0 - + + -
34T TRP* 1.3 76.6 - - - +
36T GLN* 1.3 58.6 + - - +
43T PRO* 4.4 9.4 - - + -
44T THR* 3.3 26.7 - - - +
45T PHE* 3.5 22.2 - + + -
46T LEU* 3.6 9.2 - - - +
88T TYR* 3.3 6.1 - - - +
89T LEU* 2.7 57.6 + - + -
91T ALA* 4.6 1.1 - - + -
104T PRO* 5.4 1.9 - - + +
106T PHE* 3.5 35.7 - + - -
105U PRO* 3.7 6.2 - - - +
106U GLN* 3.0 45.8 + - + +
108U PHE* 4.5 4.7 - + - -
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Residues in contact with GLN 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T TYR* 1.3 71.9 - - - +
37T GLN* 1.3 61.3 + - - +
38T HIS* 3.5 24.8 + - + +
42T ALA 4.0 1.2 - - - +
43T PRO* 3.3 1.6 - - - +
44T THR* 2.7 52.5 + - - +
46T LEU* 3.6 18.1 - - + +
62T PHE* 4.3 13.1 - - - -
83T LYS 4.4 1.8 + - - +
84T ASP* 4.4 10.9 + - - +
86T ALA* 3.8 12.2 - - + +
87T SER 3.7 2.5 - - - -
88T TYR* 2.7 42.7 + - + -
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Residues in contact with GLN 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T TYR 4.0 0.4 + - - -
36T GLN* 1.3 75.3 - - - +
38T HIS* 1.3 73.4 + - - +
39T ALA* 5.9 0.7 - - - -
40T GLY* 5.2 3.4 - - - +
41T GLU 3.3 21.8 + - - +
42T ALA 4.2 1.1 - - - -
43T PRO* 3.9 24.7 - - + +
86T ALA* 3.8 2.9 - - - -
87T SER* 2.7 54.7 + - - +
89T LEU* 3.9 15.5 - - + +
37U GLN* 2.8 45.1 + - - +
91U PHE* 3.8 11.5 - - - -
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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