Contacts of the strand formed by residues 57 - 69 (chain B) in PDB entry 5TIN
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 ASP 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B SER 4.4 2.4 - - - +
51B ILE* 3.6 2.9 - - - +
52B ALA* 2.9 33.5 + - - +
55B THR* 2.7 27.2 + - - -
56B MET* 1.3 79.2 - - - +
58B TYR* 1.3 65.3 + - - +
104B LYS* 2.9 36.8 + - + +
135B THR* 3.9 15.4 - - + +
136B LEU 3.1 16.4 - - - +
138B CYS* 3.9 6.0 + - - +
140B MET* 4.5 1.9 - - - +
59C ARG* 5.5 0.2 + - - -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.7 35.7 - + - -
49B GLY 3.9 0.2 - - - +
50B SER 3.5 8.5 - - - -
51B ILE* 3.9 24.2 - - + -
57B ASP* 1.3 76.2 - - - +
59B ARG* 1.3 62.2 + - - +
60B VAL* 3.8 20.0 - - + -
134B LEU 3.7 0.2 - - - +
135B THR* 3.3 7.8 - - - +
136B LEU* 2.8 70.1 + - + +
137B SER 4.3 0.4 - - - -
138B CYS* 3.7 17.5 - - + -
152B CYS* 3.6 22.9 - - + -
153B ILE 2.7 31.2 + - - -
154B MET 4.0 0.3 + - - -
214B PHE* 4.0 11.6 - + - -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 3.4 51.1 + - - +
47B SER* 5.2 1.5 + - - +
48B PHE* 3.5 0.3 - - - -
49B GLY 2.9 40.5 + - - +
50B SER* 3.7 25.9 + - - +
58B TYR* 1.3 76.2 - - - +
60B VAL* 1.3 74.0 + - - +
133B THR* 3.9 28.8 - - + +
134B LEU 3.2 9.2 - - - +
135B THR* 3.9 16.2 - - + +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.9 3.6 - - + -
47B SER* 3.3 8.3 - - - +
48B PHE* 3.7 28.7 - - + -
58B TYR* 3.8 16.6 - - + -
59B ARG* 1.3 83.1 - - - +
61B ASN* 1.3 59.9 + - - +
62B ILE* 3.8 22.7 - - + -
132B LEU 3.8 0.2 - - - +
133B THR* 3.4 5.8 - - - +
134B LEU* 2.9 54.8 + - + +
136B LEU* 4.0 13.5 - - + -
154B MET* 4.0 10.8 - - + -
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU 4.9 3.2 + - - -
104A LYS* 6.2 0.4 - - - +
45B ILE 3.8 0.2 - - - -
46B ASN* 2.8 50.4 + - - +
47B SER* 3.0 30.9 + - - +
60B VAL* 1.3 72.5 - - - +
62B ILE* 1.3 64.8 + - - +
63B PHE* 4.7 0.2 - - - -
109B HIS* 3.3 20.0 + - - -
131B ARG* 3.1 24.5 + - - +
132B LEU 3.3 6.2 + - - -
133B THR* 2.9 25.9 + - + +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 4.3 17.7 - - + -
44B PHE 3.2 13.5 - - - +
45B ILE* 4.3 14.4 - - + -
46B ASN 4.4 0.4 - - - +
60B VAL* 3.8 23.8 - - + -
61B ASN* 1.3 81.4 - - - +
63B PHE* 1.3 71.8 + - - +
64B LEU* 4.2 15.0 - - + +
100B PHE* 4.1 17.0 - - + -
130B ILE 3.7 0.2 - - - +
131B ARG* 3.3 5.2 - - - +
132B LEU* 2.9 46.3 + - + +
134B LEU* 4.0 21.5 - - + -
154B MET* 4.5 8.5 - - + -
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.2 14.1 - + - -
101A ALA* 6.2 0.7 - - + -
159A PHE* 3.7 28.5 - + + -
202A TYR* 3.6 40.2 - + - -
43B ILE* 3.3 7.1 - - - +
44B PHE* 2.9 44.9 + + + -
46B ASN* 4.7 14.8 - - + -
61B ASN* 4.7 4.0 - - - -
62B ILE* 1.3 81.7 - - - +
64B LEU* 1.3 60.3 + - - +
65B ARG* 3.7 32.4 - - - +
129B SER* 4.0 6.5 - - - +
130B ILE 3.5 4.0 - - - +
131B ARG* 3.7 26.2 - - + -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B CYS* 5.0 2.0 - - + -
42B ASN 4.0 3.1 - - - +
43B ILE* 4.0 20.9 - - + -
62B ILE* 3.9 11.5 - - + -
63B PHE* 1.3 70.9 - - - +
65B ARG* 1.3 66.0 + - - +
66B GLN* 3.9 20.4 + - + +
98B LEU* 3.8 17.7 - - + -
100B PHE* 4.1 9.2 - - + -
128B TYR 3.5 1.7 - - - +
129B SER* 3.1 3.8 - - - -
130B ILE* 2.8 45.8 + - + +
132B LEU* 4.2 5.2 - - + -
156B LEU* 4.0 20.4 - - + -
112C THR* 3.7 29.6 - - + -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TYR* 3.6 29.5 - - - +
203A ASN* 3.3 11.4 + - - +
204A THR* 3.8 21.2 + - + +
40B THR 3.7 0.6 - - - +
41B CYS* 3.2 8.1 - - - +
42B ASN* 2.7 79.6 + - - +
44B PHE* 3.7 23.7 - - - +
63B PHE* 3.7 21.1 - - - +
64B LEU* 1.3 74.9 - - - +
66B GLN* 1.3 63.1 + - - +
67B LYS* 5.4 0.4 - - - -
127B LEU* 4.2 11.4 - - + -
128B TYR 3.4 3.1 - - - -
129B SER* 3.2 28.9 + - - +
177B GLN* 2.9 19.4 + - - -
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 4.1 11.9 - - + +
40B THR 3.4 2.9 - - - -
41B CYS* 4.3 9.4 - - - -
64B LEU* 3.9 20.8 - - + +
65B ARG* 1.3 78.6 - - - +
67B LYS* 1.3 63.3 + - - +
68B TRP* 3.8 17.5 - - + -
96B PRO* 3.4 32.7 + - - +
98B LEU* 3.8 26.0 - - + +
126B VAL 3.8 0.5 - - - +
127B LEU* 3.6 3.3 - - - +
128B TYR* 2.8 60.3 + - + +
130B ILE* 5.2 1.2 - - - +
168B PHE* 4.8 0.2 - - - -
112C THR* 4.6 6.1 + - - +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ASN* 5.9 5.0 + - - -
38B GLN 3.7 0.7 - - - +
39B VAL* 3.3 2.8 - - - +
40B THR* 2.8 49.3 + - + +
42B ASN* 4.1 8.9 - - - +
65B ARG 5.4 0.4 - - - -
66B GLN* 1.3 79.4 - - - +
68B TRP* 1.3 66.6 + - - +
126B VAL 3.2 11.0 - - - +
127B LEU* 4.0 26.2 - - + -
171B GLN* 2.8 33.0 + - - +
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Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO* 4.3 3.1 - - + -
37B VAL* 4.0 10.5 - - + -
38B GLN 3.6 16.6 - - - +
39B VAL* 4.2 4.5 - - + -
66B GLN* 3.8 24.9 - - + -
67B LYS* 1.3 86.1 - - - +
69B ASN* 1.3 75.6 + - - +
70B ASP* 4.3 6.7 + - - +
90B LEU* 6.0 0.2 - - + -
93B ILE* 4.6 4.5 - - + -
94B TRP* 3.5 49.7 + + - -
95B LYS* 3.9 8.3 - - + -
96B PRO* 3.6 31.4 - - + -
125B ASN* 3.4 5.7 - - - +
126B VAL* 2.7 64.7 + - + +
128B TYR* 3.8 15.9 - + + -
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO* 3.4 20.1 - - - +
31B ASN* 4.9 5.0 + - - +
37B VAL* 5.0 3.9 - - - +
38B GLN 4.7 2.0 + - - -
68B TRP* 1.3 79.0 - - - +
70B ASP* 1.3 59.2 + - - +
71B PRO* 3.3 24.8 - - - +
123B ASN* 3.0 28.7 + - - +
124B GLY 3.3 1.0 - - - -
125B ASN* 2.9 30.3 + - - +
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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