Contacts of the strand formed by residues 38 - 43 (chain D) in PDB entry 4JZJ
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 GLN 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D MET* 3.4 5.1 - - - +
33D LYS* 2.9 51.2 + - + +
36D ALA* 3.3 30.8 + - + +
37D GLN* 1.3 74.3 - - - +
39D LEU* 1.3 61.4 + - - +
40D THR* 3.4 7.4 + - - +
67D TYR* 3.2 39.9 + - + +
68D CYS 3.4 4.3 - - - -
69D GLN* 2.9 25.3 + - - +
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Residues in contact with LEU 39 (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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30D LEU* 3.6 22.4 - - + -
31D ARG 3.9 1.1 - - - +
32D MET* 3.5 30.3 - - + +
37D GLN 4.3 0.4 - - - -
38D GLN* 1.3 70.7 - - - +
40D THR* 1.3 57.5 + - - +
41D TRP* 3.2 9.8 - - + -
52D CYS* 4.0 19.7 - - + -
67D TYR* 3.3 0.7 - - - -
68D CYS* 2.9 35.5 + - + +
70D PHE* 3.8 17.8 - - + -
81D TYR* 4.0 18.6 - - + -
83D VAL* 3.5 30.7 - - + -
94D ILE* 3.7 16.2 - - + -
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Residues in contact with THR 40 (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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29D ASN 4.6 0.9 - - - -
30D LEU* 3.3 7.3 - - - +
31D ARG 2.9 35.2 + - - +
33D LYS* 3.2 36.2 - - - +
38D GLN* 3.4 9.2 + - - +
39D LEU* 1.3 70.9 - - - +
41D TRP* 1.3 81.2 + - - +
66D SER* 3.2 22.4 - - - +
67D TYR* 3.9 11.1 - - + +
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Residues in contact with TRP 41 (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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27D ILE* 3.4 36.7 - - + +
28D THR 3.8 7.2 - - - +
29D ASN 3.8 11.4 - - - -
30D LEU* 4.1 12.3 - - + -
39D LEU* 3.2 20.9 - - + -
40D THR* 1.3 102.3 - - - +
42D ASP* 1.3 82.5 + - - +
43D LEU* 4.3 4.9 - - + +
50D ILE* 3.6 29.6 - - + +
52D CYS* 3.9 16.8 - - - -
62D ALA* 3.9 6.5 - - + -
65D ASN 2.9 32.4 + - - -
66D SER* 3.3 16.7 + - - +
67D TYR* 3.6 19.5 - - - -
83D VAL* 4.5 10.8 - - + -
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.6 11.3 - - - +
28D THR* 3.1 35.0 + - - +
29D ASN* 3.2 29.9 - - - +
41D TRP* 1.3 96.7 - - - +
43D LEU* 1.3 61.6 + - - +
44D ASN* 3.8 6.4 + - - +
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Residues in contact with LEU 43 (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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26D PRO 4.2 9.0 - - - +
27D ILE* 4.5 4.0 - - + -
41D TRP* 4.3 3.8 - - - +
42D ASP* 1.3 74.0 - - - +
44D ASN* 1.3 64.5 + - - +
45D ARG 4.0 13.7 - - - +
46D ASN* 5.8 0.7 - - - -
47D VAL* 3.6 29.6 - - + +
50D ILE* 4.4 9.6 - - + -
64D ASN 4.8 2.9 - - - +
65D ASN* 3.6 32.5 - - + +
66D SER* 5.3 1.6 - - - -
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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