Contacts of the strand formed by residues 55 - 68 (chain A) in PDB entry 5JTP
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLN* 5.4 2.7 - - + -
50A GLN 4.2 0.5 - - - -
51A LEU* 3.3 21.5 + - + -
52A ALA* 3.0 45.2 + - + +
53A ASP 3.1 6.5 - - - +
54A ASP* 1.3 80.8 - - - +
56A TYR* 1.3 64.2 + - - +
83A ILE* 3.9 25.8 - - + -
84A PHE 4.1 5.2 - - - +
85A SER* 5.0 12.3 - - - +
452E VAL* 5.0 0.4 - - - +
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Residues in contact with TYR 56 (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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48A SER* 3.0 29.2 + - - -
49A SER 3.3 16.8 + - - -
50A GLN* 3.6 21.9 + - + -
54A ASP 4.0 0.4 - - - -
55A VAL* 1.3 75.1 - - - +
57A GLU* 1.3 65.3 + - - +
58A VAL* 5.1 2.2 - - + -
83A ILE* 4.9 0.4 - - - -
84A PHE* 2.9 38.9 + - - +
86A ILE* 3.6 18.6 - - + -
98A LEU* 3.6 35.7 - - + -
451E VAL* 4.0 13.0 - - + +
452E VAL* 3.5 31.6 - - + -
453E GLY 4.1 0.9 - - - -
454E LEU* 3.0 35.2 + - + +
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Residues in contact with GLU 57 (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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17A TYR* 2.9 27.4 + - - -
19A LYS* 2.9 36.4 + - - +
48A SER* 3.7 4.7 + - - -
49A SER* 2.9 55.8 + - - +
51A LEU* 3.5 19.5 - - + +
56A TYR* 1.3 75.4 - - - +
58A VAL* 1.3 66.3 + - - +
59A VAL* 4.3 5.2 - - + -
82A GLY 3.4 20.3 + - - +
83A ILE* 3.6 7.5 + - - +
29B PRO* 3.5 9.6 - - - +
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Residues in contact with VAL 58 (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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46A THR* 4.2 12.1 - - + -
47A ALA 3.7 9.6 - - - +
48A SER* 5.6 2.2 - - - +
56A TYR* 5.1 5.8 - - + +
57A GLU* 1.3 79.0 - - - +
59A VAL* 1.3 65.8 + - - +
82A GLY 2.9 28.9 + - - +
84A PHE* 4.0 15.7 - - + -
98A LEU* 3.3 50.3 - - + +
102A CYS* 4.1 8.3 - - + -
103A PRO* 4.0 17.7 - - + -
106A LEU* 3.2 10.9 - - + +
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Residues in contact with VAL 59 (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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19A LYS* 3.8 29.6 - - + +
46A THR* 3.6 1.4 - - - +
47A ALA* 2.9 52.1 + - + +
48A SER 5.8 0.2 - - - -
49A SER* 5.2 4.7 - - - -
57A GLU* 4.3 12.6 - - + +
58A VAL* 1.3 78.6 - - - +
60A LEU* 1.3 60.3 + - - +
61A ARG* 3.5 3.1 + - + +
79A GLN* 3.7 49.6 - - + +
80A GLN 3.6 3.4 - - - -
81A GLY* 3.9 5.2 - - - -
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Residues in contact with LEU 60 (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 LEU* 4.8 6.1 - - + -
45A ASP 3.8 8.5 - - - +
46A THR* 3.5 22.0 - - - +
59A VAL* 1.3 68.8 - - - +
61A ARG* 1.3 59.1 + - - +
62A VAL* 3.4 27.7 + - + +
78A VAL 3.2 4.5 - - - +
79A GLN* 4.3 0.2 - - - -
80A GLN* 2.9 39.8 + - + +
103A PRO* 3.1 43.7 - - + +
106A LEU* 3.9 10.9 - - + +
107A PHE* 3.9 15.7 - - + +
110A ALA* 5.0 0.4 - - + -
133A PHE* 4.0 25.1 - - + -
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Residues in contact with ARG 61 (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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43A ASP 3.7 0.7 - - - +
44A LEU* 4.0 1.2 - - - -
45A ASP* 2.8 73.0 + - + +
46A THR 6.0 0.4 - - - -
47A ALA* 6.1 1.6 - - + +
59A VAL* 3.5 4.6 + - + +
60A LEU* 1.3 69.3 - - - +
62A VAL* 1.3 60.9 + - - +
63A THR* 3.3 19.1 + - - +
77A GLU* 2.9 40.9 + - + -
78A VAL 3.4 4.9 - - - -
79A GLN* 3.7 33.6 - - + +
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Residues in contact with VAL 62 (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 LEU* 3.5 26.0 - - + -
43A ASP 4.1 2.0 - - - -
44A LEU* 4.4 11.9 - - + -
60A LEU* 3.6 28.9 - - + +
61A ARG* 1.3 69.0 - - - +
63A THR* 1.3 57.8 + - - +
64A VAL* 4.3 0.9 - - + -
77A GLU* 3.5 1.4 - - - -
78A VAL 3.0 29.0 + - - +
107A PHE* 4.4 13.0 - - + -
110A ALA* 3.6 27.4 - - + -
111A ARG 5.6 0.7 - - - +
114A ILE* 3.5 29.6 - - + +
128A LEU* 4.9 5.2 - - + -
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Residues in contact with THR 63 (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 LEU* 3.5 2.1 - - - +
43A ASP* 2.8 67.4 + - + +
45A ASP* 5.3 1.0 - - - +
61A ARG* 3.3 24.4 + - - +
62A VAL* 1.3 69.8 - - - +
64A VAL* 1.3 60.1 + - - +
65A THR* 5.5 0.9 - - + -
75A LEU* 3.9 19.7 - - + -
76A CYS 4.1 0.2 - - - -
77A GLU* 3.1 34.4 + - + +
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Residues in contact with VAL 64 (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* 4.7 4.7 - - + -
41A LYS 3.9 3.6 - - - +
42A LEU* 3.7 20.9 - - + -
63A THR* 1.3 72.5 - - - +
65A THR* 1.3 67.5 + - - +
74A PHE* 4.0 15.5 - - + -
75A LEU* 3.0 8.6 - - - +
76A CYS* 2.9 39.2 + - + +
114A ILE* 3.7 36.3 - - + -
126A LEU* 3.4 27.6 - - + -
128A LEU* 4.1 13.5 - - + -
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Residues in contact with THR 65 (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 GLU 3.2 0.6 - - - +
40A VAL* 3.4 5.5 - - - +
41A LYS* 2.9 72.8 + - + +
43A ASP* 3.6 6.3 - - - +
63A THR* 5.5 0.9 - - + -
64A VAL* 1.3 79.1 - - - +
66A ALA* 1.3 67.9 + - - +
67A SER* 4.4 8.9 + - - +
72A THR* 4.3 9.0 - - - +
74A PHE 3.7 10.1 + - - -
75A LEU* 4.2 12.4 - - - +
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Residues in contact with ALA 66 (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 PRO* 3.8 20.6 - - + -
39A GLU 3.2 10.1 - - - +
40A VAL* 4.4 4.0 - - + -
65A THR* 1.3 75.6 + - - +
67A SER* 1.3 53.5 + - - +
72A THR* 3.6 1.9 - - - +
73A ALA* 2.8 31.5 + - + -
74A PHE* 3.0 48.8 + - + +
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Residues in contact with SER 67 (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 GLU* 3.3 38.3 + - - +
41A LYS* 5.8 2.9 - - - -
65A THR* 4.4 9.8 + - - +
66A ALA* 1.3 74.8 - - - +
68A LEU* 1.3 60.4 + - - +
69A GLY 3.2 14.2 + - - -
71A GLU 3.4 13.0 - - - -
72A THR* 3.8 18.6 - - - +
73A ALA 4.2 0.2 - - - +
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Residues in contact with LEU 68 (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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34A LYS* 6.0 4.5 - - - +
35A ASP 5.8 1.8 - - - +
37A GLN* 3.2 42.8 + - + +
38A PRO* 5.1 2.1 - - + +
39A GLU* 4.8 3.6 - - + +
66A ALA 4.4 0.2 - - - -
67A SER* 1.3 67.8 - - - +
69A GLY* 1.3 59.3 + - - +
70A GLU* 2.9 14.5 + - + +
71A GLU* 2.9 20.5 + - + +
73A ALA* 5.1 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