Contacts of the strand formed by residues 71 - 87 (chain D) 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 GLU 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D ASN* 3.1 25.1 + - - +
30D HIS* 3.0 41.5 + - + -
31D VAL* 3.6 23.7 - - + -
34D LYS* 2.9 34.4 + - - +
67D SER* 3.3 8.2 - - - -
68D LEU 2.9 28.4 + - - +
69D GLY 3.5 0.2 - - - -
70D GLU* 1.3 90.9 - - - +
72D THR* 1.3 58.8 + - - +
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Residues in contact with THR 72 (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* 3.8 24.8 - - + +
27D ASN* 3.0 24.9 + - - +
31D VAL* 3.5 8.3 - - - +
65D THR* 5.2 2.6 - - + +
66D ALA 3.2 16.8 - - - +
67D SER* 3.6 10.9 + - - +
71D GLU* 1.3 73.1 - - - +
73D ALA* 1.3 61.5 + - - +
74D PHE 4.0 2.9 - - - +
75D LEU* 3.7 29.6 - - + -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA* 3.9 0.9 - - - -
26D PRO* 3.5 15.1 - - - +
31D VAL* 3.7 12.3 - - - +
38D PRO* 3.5 34.5 - - + -
66D ALA 3.0 8.8 + - - +
67D SER* 3.4 4.3 - - - +
68D LEU* 3.7 24.5 - - + +
72D THR* 1.3 73.9 - - - +
74D PHE* 1.3 60.5 + - + +
123D PHE* 3.1 22.2 - - + -
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Residues in contact with PHE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.8 25.8 - + + -
24D GLU 3.6 5.4 - - - -
26D PRO* 4.5 0.7 - - - -
37D GLN* 5.0 3.1 - - - -
38D PRO* 3.7 22.0 - - + -
40D VAL* 3.9 13.9 - - + -
64D VAL* 3.7 26.3 - - + +
66D ALA* 2.9 53.0 + - + +
72D THR 4.0 0.2 - - - -
73D ALA* 1.3 80.6 - - - +
75D LEU* 1.3 65.5 + - - +
76D CYS* 4.8 1.3 - - + -
118D VAL* 3.6 28.3 - - + -
123D PHE* 3.7 44.4 - + + -
124D PRO 5.2 1.1 - - - -
126D LEU* 4.2 7.0 - - + -
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Residues in contact with LEU 75 (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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22D SER 4.3 1.1 - - - -
23D PHE* 3.2 11.7 - - - -
24D GLU* 2.8 62.9 + - + +
26D PRO* 4.7 8.3 - - + -
64D VAL 3.6 1.6 - - - -
65D THR* 3.7 36.1 - - + +
72D THR* 3.7 24.9 - - + +
74D PHE* 1.3 75.8 - - - +
76D CYS* 1.3 61.6 + - - +
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Residues in contact with CYS 76 (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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22D SER 3.2 6.9 + - - -
23D PHE* 4.2 9.2 - - + -
63D THR* 3.4 4.5 - - - +
64D VAL* 2.8 39.2 + - + +
74D PHE* 4.8 4.7 - - + -
75D LEU* 1.3 76.4 - - - +
77D GLU* 1.3 64.7 + - - +
78D VAL* 4.3 0.2 - - - -
114D ILE* 3.4 42.6 - - + -
117D MET* 3.2 34.1 - - - -
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASP* 4.3 12.4 - - - +
21D ILE* 3.5 2.3 - - - -
22D SER* 2.9 41.0 + - - +
61D ARG* 3.0 46.1 + - + +
62D VAL 3.3 7.2 - - - +
63D THR* 3.0 32.8 + - + +
76D CYS* 1.3 77.5 - - - +
78D VAL* 1.3 66.3 + - - +
79D GLN* 4.3 0.6 - - - +
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Residues in contact with VAL 78 (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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18D THR* 3.8 5.8 - - + -
20D ASP 3.4 11.0 - - - +
21D ILE* 4.3 3.4 - - + -
60D LEU 3.0 13.5 - - - +
61D ARG* 4.4 0.4 - - - -
62D VAL* 3.0 25.6 + - + +
77D GLU* 1.3 79.1 - - - +
79D GLN* 1.3 62.0 + - - +
80D GLN* 3.4 34.6 + - + +
110D ALA* 4.6 4.9 - - - +
113D CYS* 3.6 29.6 - - + -
114D ILE* 3.8 18.4 - - + -
117D MET* 3.6 19.7 - - + -
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Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D THR* 3.8 0.5 - - - -
19D LYS* 3.0 31.3 + - + +
20D ASP* 2.9 47.0 + - + +
47D ALA* 5.9 1.6 - - - +
59D VAL* 3.7 22.8 - - + +
60D LEU 3.3 5.8 - - - -
61D ARG* 3.1 53.0 + - + +
77D GLU* 4.3 0.8 - - - +
78D VAL* 1.3 70.4 - - - +
80D GLN* 1.3 60.2 + - - +
81D GLY 3.2 3.6 + - - -
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Residues in contact with GLN 80 (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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120C ARG 5.2 0.2 - - - +
16D ILE* 3.2 24.2 - - + +
17D TYR* 3.6 11.5 - - - +
18D THR* 3.3 26.0 - - - +
60D LEU* 2.8 32.3 + - + +
78D VAL* 3.4 13.3 + - + +
79D GLN* 1.3 68.3 - - - +
81D GLY* 1.3 59.2 + - - +
106D LEU* 3.4 47.3 - - + +
109D TYR* 3.3 32.0 + - + +
110D ALA* 3.8 9.6 - - + +
113D CYS* 4.0 2.2 - - - +
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Residues in contact with GLY 81 (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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16D ILE* 3.9 1.0 - - - -
17D TYR* 2.8 49.0 + - - +
19D LYS* 3.9 23.1 - - - +
57D GLU* 4.8 0.4 - - - -
58D VAL 3.4 7.4 - - - -
59D VAL* 4.0 5.6 - - - -
79D GLN 3.2 7.7 + - - -
80D GLN* 1.3 72.8 - - - +
82D GLY* 1.3 57.5 + - - -
106D LEU* 3.9 2.2 - - - +
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Residues in contact with GLY 82 (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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15D ARG 3.3 10.8 - - - -
16D ILE* 4.5 0.4 - - - -
57D GLU* 3.2 6.7 - - - +
58D VAL 2.9 33.2 + - - -
81D GLY* 1.3 74.0 - - - -
83D ILE* 1.3 63.9 + - - -
84D PHE* 3.3 13.8 - - - -
106D LEU* 3.7 17.6 - - - +
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Residues in contact with ILE 83 (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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29C PRO* 4.4 9.0 - - + -
32C PHE* 5.2 1.1 - - + -
13D ILE 3.7 1.0 - - - -
14D GLN* 2.9 61.8 + - + +
15D ARG* 2.9 26.9 + - + +
17D TYR* 3.6 36.8 - - + +
51D LEU* 3.7 20.9 - - + -
55D VAL* 3.7 15.5 - - + -
56D TYR 4.1 2.2 - - - -
57D GLU* 4.4 3.4 - - - +
82D GLY* 1.3 71.3 - - - -
84D PHE* 1.4 64.3 + - - +
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Residues in contact with PHE 84 (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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11D PHE* 3.6 39.9 - + + -
12D GLN 3.7 4.5 - - - +
13D ILE* 3.9 20.0 - - + -
14D GLN* 4.5 2.5 - - - -
16D ILE* 4.9 0.9 - - + -
56D TYR* 2.9 41.1 + - - +
58D VAL* 3.9 21.1 - - + -
82D GLY* 3.3 30.3 - - - -
83D ILE* 1.4 77.6 - - - +
85D SER* 1.3 59.6 + - - +
86D ILE* 3.5 9.7 + - + +
98D LEU* 5.3 0.4 - - + -
102D CYS* 3.7 33.9 - - + -
105D ILE* 3.9 22.0 - - + -
106D LEU* 4.0 17.3 - - + -
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Residues in contact with SER 85 (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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10D THR* 3.6 6.3 - - - +
11D PHE* 3.1 9.9 + - - -
12D GLN* 2.9 51.3 + - - +
14D GLN* 2.8 35.6 + - - +
54D ASP* 3.3 12.6 - - - -
55D VAL* 4.2 6.0 - - - +
84D PHE* 1.3 67.7 - - - +
86D ILE* 1.3 59.8 + - - +
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Residues in contact with ILE 86 (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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10D THR* 3.6 4.5 - - - -
11D PHE* 3.8 30.5 - - + -
50D GLN* 5.9 0.2 - - - +
54D ASP* 2.8 35.8 + - - +
56D TYR* 3.7 30.3 - - + -
84D PHE* 4.0 12.1 - - + +
85D SER* 1.3 74.0 - - - +
87D ALA* 1.3 64.8 + - - +
89D ILE* 4.2 11.7 - - + -
94D MET* 3.3 36.8 - - + -
97D CYS* 5.1 2.5 - - - -
98D LEU* 4.1 10.3 - - + -
451H VAL* 4.4 14.3 - - + +
452H VAL* 5.4 0.2 - - + -
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Residues in contact with ALA 87 (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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4D GLN* 4.8 1.3 - - - +
5D ASN* 3.3 42.6 - - + +
9D MET* 3.7 1.9 - - - +
10D THR* 2.9 38.5 + - + +
54D ASP* 3.9 5.4 - - + +
86D ILE* 1.3 76.3 - - - +
88D GLY* 1.3 59.7 + - - +
89D ILE* 3.1 21.8 + - - +
451H VAL* 5.4 4.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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