Contacts of the strand formed by residues 38 - 47 (chain A) in PDB entry 1J71
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 LEU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.3 18.6 - - + -
20A VAL* 5.9 0.7 - - + -
29A VAL* 4.7 2.2 - - + -
36A SER 4.3 0.4 + - - -
37A ASP* 1.3 75.7 - - - +
39A TRP* 1.3 73.8 + - - +
40A VAL* 4.7 4.5 - - + -
94A PHE* 5.3 0.2 - - - -
99A VAL* 4.3 26.9 - - + -
109A GLN* 4.8 2.5 - - + +
110A GLN 5.0 2.4 + - - +
111A PHE* 3.3 27.3 - - + +
112A ALA* 3.0 21.5 + - - +
123A ILE 3.3 13.5 - - - +
124A MET* 3.7 28.7 - - + +
125A GLY 4.6 1.3 + - - +
138A TYR* 4.2 4.3 + - - -
140A ASN* 5.9 2.2 - - + +
141A VAL* 4.0 26.2 - - + -
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Residues in contact with TRP 39 (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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29A VAL* 4.4 0.3 - - - +
37A ASP* 4.3 6.1 - - + -
38A LEU* 1.3 78.6 - - - +
40A VAL* 1.3 68.9 + - - +
41A VAL* 3.8 23.3 - - + -
80A PHE* 4.1 17.7 - + + -
82A ILE* 4.6 0.2 - - - +
84A TYR* 2.9 28.0 + - - -
90A SER* 3.1 23.0 + - - -
111A PHE* 5.0 0.4 - - - -
112A ALA* 3.1 21.5 - - + +
114A VAL* 3.3 39.5 - - + -
117A THR* 3.7 12.1 - - + -
119A VAL* 3.8 15.5 - - + -
121A GLN 3.3 25.4 - - - -
122A GLY* 3.4 5.3 - - - -
123A ILE* 3.0 50.3 + - + +
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Residues in contact with VAL 40 (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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18A ILE* 4.6 5.2 - - + -
20A VAL* 4.4 12.3 - - + -
27A GLN* 4.2 26.2 - - + +
29A VAL* 4.6 11.0 - - + -
38A LEU* 4.7 5.2 - - + -
39A TRP* 1.3 85.5 - - - +
41A VAL* 1.3 58.8 + - - +
42A ASP 3.6 0.2 + - - -
65A PHE* 3.6 31.2 - - + -
111A PHE* 3.9 21.3 - - + -
112A ALA 2.9 10.5 + - - +
113A ASP* 4.2 2.5 - - - +
114A VAL* 2.8 28.9 + - - +
122A GLY* 4.5 3.6 - - - -
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Residues in contact with VAL 41 (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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27A GLN* 4.9 2.8 - - - +
39A TRP* 3.8 21.5 - - + -
40A VAL* 1.3 71.7 - - - +
42A ASP* 1.3 67.4 + - - +
45A ALA* 3.7 15.5 - - + -
59A CYS* 3.5 40.2 - - + +
60A LYS* 4.2 8.3 - - + -
63A GLY 4.2 12.3 - - - +
64A THR* 3.1 4.6 - - + -
65A PHE* 2.7 30.9 + - - -
113A ASP* 4.3 0.9 - - - -
114A VAL* 3.9 3.6 - - - +
117A THR* 5.0 2.7 - - + -
121A GLN* 4.4 3.1 - - - -
122A GLY* 4.0 15.0 - - - +
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Residues in contact with ASP 42 (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 VAL 3.6 2.0 + - - -
41A VAL* 1.3 79.2 - - - +
43A THR* 1.3 68.2 + - - +
44A ASP* 2.9 34.5 + - - +
45A ALA* 2.9 18.9 + - - +
60A LYS* 4.2 1.2 - - - -
64A THR* 4.1 1.1 - - - -
65A PHE 3.4 5.4 - - - -
67A PRO* 3.4 17.6 - - - +
113A ASP* 2.5 33.7 + - - +
114A VAL 2.8 22.5 + - - +
115A THR* 3.9 17.1 - - + +
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Residues in contact with THR 43 (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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25A GLN* 5.1 0.2 + - - -
41A VAL 3.6 0.6 + - - -
42A ASP* 1.3 73.2 - - - +
44A ASP* 1.3 69.7 + - - +
60A LYS* 3.0 22.3 + - - +
64A THR* 3.2 26.9 + - - +
65A PHE 2.9 18.2 + - - -
66A ASP* 3.4 22.9 - - + +
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Residues in contact with ASP 44 (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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42A ASP* 2.9 16.1 + - - +
43A THR* 1.3 89.3 - - - +
45A ALA* 1.3 65.6 + - - +
46A GLU* 3.8 6.6 + - - +
60A LYS* 3.8 3.4 - - - +
115A THR* 4.6 3.3 - - + +
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Residues in contact with ALA 45 (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 16.6 - - + -
42A ASP* 2.9 19.0 + - - +
43A THR 3.4 1.0 - - - -
44A ASP* 1.3 79.4 - - - +
46A GLU* 1.3 63.9 + - - +
47A CYS 3.8 0.7 + - - -
57A ASN* 4.5 1.4 + - - -
59A CYS* 4.8 2.2 - - - -
60A LYS* 2.9 27.3 + - - +
114A VAL 3.4 21.8 - - - +
115A THR* 3.2 14.4 - - - +
116A THR* 4.6 0.4 - - - +
117A THR* 5.4 2.5 - - + -
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Residues in contact with GLU 46 (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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44A ASP 4.5 5.4 - - - +
45A ALA* 1.3 75.1 - - - +
47A CYS* 1.3 62.6 + - - +
48A GLN* 3.4 5.9 + - + +
57A ASN* 5.8 0.2 - - - +
59A CYS* 4.7 1.1 - - - -
115A THR* 2.7 15.6 + - - +
116A THR* 3.3 25.6 + - + +
117A THR* 3.2 24.4 + - - +
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Residues in contact with CYS 47 (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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45A ALA 3.8 0.6 + - - -
46A GLU* 1.3 72.0 - - - +
48A GLN* 1.3 62.0 + - - +
49A VAL* 3.5 6.1 + - - +
56A ASN* 3.5 21.9 + - - +
57A ASN* 3.8 19.8 - - - +
58A PHE* 3.6 18.3 - - + -
59A CYS* 2.0 56.8 - - + -
60A LYS* 4.0 10.5 - - - -
117A THR 3.5 4.9 - - - -
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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