Contacts of the strand formed by residues 21 - 27 (chain B) in PDB entry 4NTX
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 VAL 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A PRO* 5.0 0.9 - - - -
19B ALA* 4.9 1.1 - - + +
20B PHE* 1.3 75.8 - - - +
22B ASP* 1.3 79.9 + - + +
23B SER* 3.4 0.8 + - - -
37B PHE* 3.5 9.6 - - - -
38B TYR* 2.9 50.0 + - + +
40B GLN* 3.9 16.6 - - - +
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Residues in contact with ASP 22 (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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286A PRO* 6.0 0.2 - - - +
21B VAL* 1.3 89.3 - - + +
23B SER* 1.3 62.0 + - - +
24B TYR* 4.5 11.7 - - + +
35B HIS* 2.6 34.6 + - + +
36B PHE 3.9 0.7 - - - -
37B PHE* 3.3 16.1 - - - -
48B PHE 4.8 0.3 - - - +
49B THR* 4.7 9.6 - - - +
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Residues in contact with SER 23 (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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21B VAL* 5.0 0.7 - - - -
22B ASP* 1.3 76.1 - - - +
24B TYR* 1.3 85.4 + - - +
35B HIS* 3.4 1.6 - - - -
36B PHE* 2.9 52.1 + - - -
38B TYR* 3.5 21.6 - - - +
47B HIS* 3.4 16.3 - - - +
48B PHE 3.1 15.5 + - - -
49B THR* 5.6 0.2 - - - -
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Residues in contact with TYR 24 (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 ASP* 4.5 9.2 - - + +
23B SER* 1.3 103.3 + - - +
25B TYR* 1.3 60.2 + - - +
33B CYS* 4.9 0.2 - - + -
34B VAL 3.4 5.8 - - - +
35B HIS* 3.6 40.6 - + + -
36B PHE* 4.0 2.7 - - - -
47B HIS* 3.3 4.0 - - - -
48B PHE* 2.8 40.0 + - - +
49B THR 3.6 15.3 - - - -
50B THR* 3.4 30.1 - - - +
51B MET* 3.7 39.5 - - + -
54B CYS* 4.0 11.4 - - + -
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Residues in contact with TYR 25 (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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358A GLU* 3.4 23.9 + - - +
361A VAL* 5.0 4.7 + - - +
11B PRO* 3.5 26.2 - - + -
13B PHE* 3.6 27.8 - + - -
24B TYR* 1.3 72.8 - - - +
26B PHE* 1.3 80.0 + - - +
27B ASN* 3.0 28.9 + - - -
30B ARG* 5.7 0.5 + - - -
33B CYS* 3.1 1.9 - - - -
34B VAL* 2.8 74.7 + - + +
36B PHE* 3.6 22.9 - + + -
46B ASN* 3.3 27.1 - - - +
54B CYS* 3.3 6.3 - - - -
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Residues in contact with PHE 26 (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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358A GLU* 3.8 2.9 - - - +
3B ARG* 3.4 30.7 - - - -
7B CYS* 3.2 30.7 - - + +
8B TYR* 4.7 4.5 - + - -
25B TYR* 1.3 83.0 - - - +
27B ASN* 1.3 61.1 + - - +
28B ARG* 3.5 25.4 + - + -
31B ILE* 3.7 22.7 - - + -
32B THR* 3.7 23.3 - - - -
33B CYS* 3.7 9.2 - - - -
46B ASN* 2.9 21.5 + - - +
54B CYS* 3.4 1.4 - - - -
58B CYS* 3.2 45.3 - - + -
59B HIS* 4.0 6.7 - + - -
70C CYS* 5.6 0.9 - - - -
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Residues in contact with ASN 27 (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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358A GLU* 2.9 32.9 + - - +
359A TYR 3.7 9.5 + - - -
361A VAL 5.9 0.2 - - - +
25B TYR* 3.0 27.3 + - + -
26B PHE* 1.3 71.9 - - - +
28B ARG* 1.3 58.4 + - - +
29B SER* 2.8 33.8 + - - -
30B ARG* 3.0 23.0 + - + +
31B ILE* 2.9 28.9 + - - -
32B THR 2.9 18.5 + - - +
34B VAL* 4.0 13.1 - - + +
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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