Contacts of the strand formed by residues 71 - 87 (chain A) in PDB entry 5JTO
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 GLU 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 3.3 36.4 - - + +
30A HIS* 3.1 36.6 + - - +
31A VAL* 3.4 15.3 + - + +
34A LYS* 2.9 37.3 + - + +
67A SER* 4.1 1.6 - - - -
68A LEU* 2.8 35.6 + - + +
69A GLY 3.8 0.4 - - - -
70A GLU* 1.3 84.5 - - + +
72A THR* 1.4 58.9 + - - +
73A ALA 3.6 0.3 + - - -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 3.9 24.6 - - + +
27A ASN* 3.1 30.1 + - - +
31A VAL* 3.5 8.2 - - - +
65A THR* 4.7 9.3 - - + +
66A ALA 3.2 19.3 - - - +
67A SER* 3.0 15.1 + - - +
70A GLU 4.0 2.7 + - - -
71A GLU* 1.4 70.1 - - - +
73A ALA* 1.3 61.6 + - - +
74A PHE 3.7 18.8 - - - +
75A LEU* 5.2 2.7 - - + -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.2 26.3 - - - +
26A PRO* 3.7 1.5 - - - +
28A ALA* 4.4 5.4 + - - -
31A VAL* 3.6 21.9 - - + +
66A ALA* 2.8 14.9 + - + +
68A LEU* 3.5 24.5 - - + -
71A GLU 3.6 3.2 + - - -
72A THR* 1.3 73.5 - - - +
74A PHE* 1.3 73.7 + - + +
123A PHE* 3.9 10.5 - - + -
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.8 20.6 - + + -
24A GLU 3.1 11.7 - - - +
25A ALA* 4.1 1.8 - - + +
26A PRO* 4.4 0.9 - - - -
40A VAL* 5.5 0.7 - - + -
64A VAL* 3.7 28.0 - - + -
65A THR* 3.8 0.9 - - - -
66A ALA* 3.1 46.8 + - + +
72A THR* 3.7 7.5 - - - +
73A ALA* 1.3 88.3 - - + +
75A LEU* 1.3 61.4 + - - +
76A CYS* 3.3 35.4 - - - -
118A VAL* 3.7 20.2 - - + -
123A PHE* 3.5 39.5 - + + -
126A LEU* 4.7 6.1 - - + -
296E THR* 5.2 4.3 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.5 6.1 - - - +
23A PHE* 3.2 7.4 + - - -
24A GLU* 2.7 60.3 + - + +
26A PRO* 5.6 1.3 - - + -
63A THR* 3.5 20.6 - - + -
64A VAL 3.2 8.1 - - - +
65A THR* 3.3 35.4 - - + +
72A THR* 5.2 3.6 - - + -
74A PHE* 1.3 75.8 - - - +
76A CYS* 1.3 60.2 + - - +
77A GLU* 5.0 9.2 - - + +
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Residues in contact with CYS 76 (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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22A SER 3.7 3.8 - - - -
23A PHE* 3.3 21.3 - - - -
62A VAL 3.1 7.4 - - - +
63A THR* 4.9 0.4 - - - -
64A VAL* 2.8 40.5 + - + +
74A PHE* 3.3 24.9 - - - -
75A LEU* 1.3 68.8 - - - +
77A GLU* 1.3 58.0 + - - +
78A VAL 4.1 0.2 - - - -
114A ILE* 3.6 24.0 - - + +
117A MET* 3.7 14.1 - - + -
118A VAL* 3.4 22.2 - - - -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP* 4.5 11.0 - - - +
21A ILE* 3.7 1.2 - - - -
22A SER* 2.8 57.5 + - - +
61A ARG* 3.0 47.1 + - + -
62A VAL 3.4 4.0 - - - -
63A THR* 3.1 32.6 + - + +
75A LEU* 3.8 10.6 + - + +
76A CYS* 1.3 71.2 - - - +
78A VAL* 1.3 58.9 + - - +
79A GLN* 4.2 1.1 + - - -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 4.0 14.4 - - + -
20A ASP 3.7 4.7 - - - +
21A ILE* 4.7 2.9 - - + -
60A LEU 2.9 15.4 - - - +
61A ARG* 4.2 0.2 - - - -
62A VAL* 3.0 22.7 + - - +
77A GLU* 1.3 79.1 - - - +
79A GLN* 1.3 60.3 + - - +
80A GLN* 3.2 13.7 + - - +
110A ALA* 4.3 7.4 - - - -
113A CYS* 3.6 35.4 - - + -
114A ILE* 3.6 22.9 - - + -
117A MET* 3.5 29.2 - - + -
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Residues in contact with GLN 79 (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 THR* 3.7 0.9 - - - -
19A LYS* 3.0 28.7 + - + +
20A ASP* 2.9 52.9 + - + +
59A VAL* 3.7 19.2 - - + +
60A LEU 3.4 6.1 - - - -
61A ARG* 3.7 37.3 - - + +
77A GLU* 4.2 2.5 + - + -
78A VAL* 1.3 68.1 - - - +
80A GLN* 1.3 60.4 + - - +
81A GLY 3.3 2.1 + - - -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.4 1.4 - - - +
17A TYR* 3.5 29.2 + - - -
18A THR* 3.3 25.2 - - - +
59A VAL* 3.4 1.8 - - - -
60A LEU* 3.1 31.1 + - + +
78A VAL* 3.2 4.4 + - + +
79A GLN* 1.3 69.5 - - - +
81A GLY* 1.3 58.4 + - - +
106A LEU* 3.4 44.2 - - + +
109A TYR* 3.4 41.1 + - + +
110A ALA* 3.6 20.8 - - + +
113A CYS* 4.4 0.2 - - - +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 2.8 39.5 + - - +
19A LYS* 4.0 11.4 - - - +
58A VAL 3.3 8.1 - - - -
59A VAL* 3.9 14.8 - - - -
79A GLN 3.3 6.1 + - - -
80A GLN* 1.3 73.9 - - - +
82A GLY* 1.3 57.4 + - - -
106A LEU* 3.5 11.5 - - - +
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Residues in contact with GLY 82 (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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15A ARG 3.6 9.6 - - - -
16A ILE* 4.2 0.7 - - - -
17A TYR* 5.0 1.5 - - - -
57A GLU* 3.3 6.2 - - - +
58A VAL 2.9 33.7 + - - -
81A GLY* 1.3 72.9 - - - -
83A ILE* 1.3 63.9 + - - -
84A PHE* 3.2 15.6 - - - -
106A LEU* 3.8 17.3 - - - -
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Residues in contact with ILE 83 (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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13A ILE* 3.6 0.5 - - - -
14A GLN* 3.1 39.7 + - + -
15A ARG* 2.8 34.5 + - + +
17A TYR* 3.8 33.0 - - + +
51A LEU* 3.6 22.7 - - + -
55A VAL* 3.6 28.3 - - + -
56A TYR 5.3 0.2 - - - +
57A GLU* 4.4 5.4 - - - +
82A GLY* 1.3 71.4 - - - -
84A PHE* 1.3 69.9 + - - +
85A SER 5.2 0.2 - - - +
29B PRO* 4.6 8.3 - - + -
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Residues in contact with PHE 84 (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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11A PHE* 3.6 23.3 - + + -
12A GLN 3.8 3.8 - - - -
13A ILE* 3.5 40.8 - - + -
16A ILE* 4.5 1.6 - - + -
55A VAL* 4.6 1.1 - - - -
56A TYR* 2.7 41.2 + - - +
58A VAL* 3.5 33.4 - - + -
82A GLY* 3.2 25.4 - - - -
83A ILE* 1.3 82.7 - - - +
85A SER* 1.3 59.0 + - - +
86A ILE* 3.3 11.2 + - + +
102A CYS* 3.8 20.2 - - + -
105A ILE* 3.9 7.4 - - + -
106A LEU* 3.7 31.2 - - + -
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Residues in contact with SER 85 (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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10A THR* 3.6 4.5 - - - +
11A PHE* 3.4 5.4 + - - -
12A GLN* 2.9 49.2 + - - +
14A GLN* 5.3 3.5 - - - +
54A ASP* 3.2 19.3 + - - +
55A VAL* 4.2 15.9 - - - +
83A ILE* 4.3 1.2 - - - +
84A PHE* 1.3 69.0 - - - +
86A ILE* 1.3 57.9 + - - +
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Residues in contact with ILE 86 (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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10A THR 3.2 8.1 - - - +
11A PHE* 3.6 33.2 - - + -
54A ASP* 2.9 27.4 + - - +
56A TYR* 3.7 40.9 - - + +
84A PHE* 3.3 8.0 + - + +
85A SER* 1.3 72.8 - - - +
87A ALA* 1.3 60.4 + - - +
89A ILE* 3.9 26.9 - - + +
94A MET* 6.0 0.2 - - + -
97A CYS* 4.2 18.4 - - - -
98A LEU* 4.0 26.5 - - + -
102A CYS* 4.7 0.9 - - - -
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Residues in contact with ALA 87 (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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9A MET* 3.2 3.5 - - - -
10A THR* 2.9 39.8 + - - +
54A ASP* 3.5 26.0 - - + +
86A ILE* 1.3 75.1 - - - +
88A GLY* 1.3 61.6 + - - +
89A ILE* 3.2 16.2 + - - +
277E LEU* 6.1 1.1 - - - -
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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