Contacts of the strand formed by residues 38 - 44 (chain B) in PDB entry 1NRX
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 THR 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER* 3.0 14.8 + - - -
37B THR* 1.3 92.4 + - - +
39B TYR* 1.3 68.5 + - - +
40B VAL* 4.2 4.3 - - + -
71B ARG* 3.0 46.8 + - + +
73B LEU* 4.1 6.1 - - + -
103B CYS* 4.0 20.2 - - - -
104B GLY 4.9 1.7 + - - -
106B ASP* 4.2 4.3 + - - -
107B THR* 4.0 15.0 - - - +
108B VAL 3.1 17.5 + - - -
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.8 38.4 - - + -
31B ILE* 3.3 22.4 - - + +
34B CYS 2.7 28.5 + - - -
36B SER* 3.0 39.9 + - - -
38B THR* 1.3 79.4 - - - +
40B VAL* 1.3 61.9 + - - +
59B PHE* 3.9 13.2 - + + -
70B PRO* 3.7 12.8 - - + -
71B ARG 2.9 20.8 + - - +
72B LEU* 3.3 19.3 - - + +
73B LEU 2.8 25.8 + - - -
108B VAL* 3.4 22.2 - - + +
110B ILE* 4.3 3.8 - - + -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 4.2 1.5 - - + -
39B TYR* 1.3 72.6 - - - +
41B LEU* 1.3 61.6 + - - +
42B VAL* 4.0 19.1 - - + -
73B LEU* 3.2 8.1 - - + +
75B TYR* 5.0 0.7 - - + -
92B ILE* 5.9 0.2 - - + -
95B TRP* 3.5 29.4 - - + -
96B MET* 4.2 17.5 - - - -
103B CYS* 3.7 30.1 - - - -
107B THR* 4.1 15.9 - - + +
108B VAL 3.3 7.5 + - - -
109B VAL* 3.4 13.0 - - + +
110B ILE* 2.8 28.2 + - - -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 4.5 5.4 - - + -
39B TYR 3.7 1.4 + - - -
40B VAL* 1.3 73.6 - - - +
42B VAL* 1.3 63.0 + - - +
43B THR* 5.1 2.0 - - + -
52B THR* 4.7 10.8 - - + +
55B PHE* 4.4 22.4 - - + -
72B LEU* 4.1 9.9 - - + -
73B LEU 2.7 13.3 + - - +
74B ILE* 3.4 27.8 - - + -
75B TYR* 2.6 35.9 + - - +
110B ILE* 3.1 33.9 - - + +
112B LEU* 3.5 39.0 - - + -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 4.0 17.5 - - + -
41B LEU* 1.3 80.9 - - - +
43B THR* 1.3 70.2 + - - +
75B TYR* 3.4 18.8 - - + +
77B ARG* 5.4 2.2 - - + -
92B ILE* 4.2 30.1 - - + -
109B VAL* 4.3 3.4 - - + -
110B ILE 3.0 5.8 + - - +
112B LEU* 3.0 27.9 + - - +
117B ILE* 3.6 10.5 - - + +
120B LEU* 5.4 1.1 - - + -
121B THR* 3.6 40.4 - - + +
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 5.1 5.2 - - + -
42B VAL* 1.3 76.7 - - - +
44B ASP* 1.3 65.9 + - - +
47B ILE* 2.8 30.5 - - - +
48B GLY* 3.6 15.5 - - - -
52B THR* 4.2 6.1 - - - +
74B ILE* 5.3 2.0 - - + -
75B TYR 3.1 5.3 + - - +
76B ASN* 3.3 25.1 - - - +
77B ARG* 2.8 23.4 + - - +
112B LEU* 2.8 24.8 + - + -
117B ILE* 3.6 14.0 - - - +
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 1.3 79.4 + - - +
45B THR* 1.3 51.7 + - - +
46B ASN 2.8 2.4 + - - -
47B ILE* 2.6 30.1 + - - +
48B GLY* 2.5 30.5 + - - -
76B ASN* 4.2 3.1 - - - -
77B ARG 2.9 16.2 - - - +
78B PRO 4.1 2.2 - - - +
79B PRO* 3.2 31.5 - - + +
80B GLY 4.6 0.3 + - - -
117B ILE* 3.7 15.8 - - + +
401B NAD 2.8 24.5 + - - -
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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