Contacts of the strand formed by residues 48 - 54 (chain A) in PDB entry 4EEJ
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 ASN 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ASP* 3.7 1.6 - - - +
44A GLN* 3.4 2.8 - - - -
45A ASP* 2.9 46.7 + - + +
46A GLY 3.2 0.2 - - - -
47A ASP* 1.3 81.5 - - - +
49A PHE* 1.3 60.8 + - - +
50A LYS* 5.9 4.7 - - - +
64A PHE 3.6 3.1 + - - +
65A THR* 2.8 37.6 + - - +
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 4.2 6.5 - - + -
42A ILE* 3.9 23.8 - - + -
43A ASP 3.2 3.6 - - - -
44A GLN* 3.5 44.2 - - + -
46A GLY 4.4 4.9 - - - -
47A ASP 3.7 7.2 - - - -
48A ASN* 1.3 82.0 - - - +
50A LYS* 1.3 64.8 + - - +
51A VAL* 4.5 4.7 - - + -
63A ASP* 3.3 4.5 - - - +
64A PHE* 2.9 70.3 + + + +
66A VAL* 3.6 21.3 - - + -
88A TRP* 4.1 10.5 - + - -
93A LEU* 3.8 24.5 - - + -
108A LYS* 5.8 0.7 - - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL 3.7 1.4 - - - +
42A ILE* 3.6 2.8 - - - -
43A ASP* 2.7 53.3 + - + +
48A ASN* 5.8 5.6 - - + +
49A PHE* 1.3 78.2 - - - +
51A VAL* 1.3 61.6 + - - +
52A LYS* 5.0 16.1 - - - +
63A ASP* 3.4 32.7 - - - +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.5 28.3 - - + -
41A VAL 3.5 3.1 - - - +
42A ILE* 4.3 11.7 - - + -
49A PHE* 4.5 9.9 - - + -
50A LYS* 1.3 75.4 - - - +
52A LYS* 1.3 72.2 + - - +
53A CYS 4.9 0.4 - - - +
60A TYR* 3.9 2.6 - - + +
61A ASP* 3.3 2.1 - - - +
62A VAL* 2.8 49.2 + - + +
63A ASP* 4.1 0.7 + - - +
64A PHE* 3.9 28.0 - - + -
106A TRP* 5.8 0.2 - - + -
108A LYS* 4.8 8.1 - - - +
201A RET 4.1 19.7 - - + -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR 3.6 1.4 - - - +
40A LEU* 3.4 4.8 - - - +
41A VAL* 2.8 54.2 + - + +
50A LYS* 5.0 18.3 - - + +
51A VAL* 1.3 83.4 - - - +
53A CYS* 1.3 60.4 + - - +
54A THR* 4.0 10.7 + - + +
61A ASP* 3.5 29.4 - - + +
63A ASP* 5.4 3.6 - - - +
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Residues in contact with CYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.0 40.2 - - - -
39A THR 3.4 7.4 - - - +
40A LEU* 4.4 14.6 - - + +
51A VAL* 4.2 0.8 - - + -
52A LYS* 1.3 74.1 - - - +
54A THR* 1.3 65.1 + - - +
59A ASN* 3.3 3.3 - - - -
60A TYR* 2.8 42.3 + - + +
61A ASP* 3.9 0.4 + - - +
130A PHE* 5.8 1.6 - - - -
201A RET 4.0 38.6 - - + +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR 4.1 0.5 - - - +
38A GLN* 3.6 5.6 - - - -
39A THR* 2.9 47.1 + - - +
41A VAL* 5.6 5.5 - - + +
52A LYS* 4.3 15.0 - - + -
53A CYS* 1.3 86.1 - - - +
55A SER* 1.3 61.6 + - - +
58A TRP 4.0 0.4 - - - -
59A ASN* 3.4 23.6 - - + +
61A ASP* 5.0 1.1 - - - +
201A RET 5.5 0.4 - - - -
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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