Contacts of the strand formed by residues 37 - 52 (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 VAL 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 3.7 10.1 - - - +
30B PRO* 3.4 44.9 - - + +
31B ASN* 5.8 2.0 - - + +
36B PRO* 1.3 70.8 - - - +
38B GLN* 1.3 60.7 + - - +
39B VAL* 3.6 19.0 + - + -
68B TRP* 4.0 19.1 - - + -
69B ASN 5.0 3.6 - - - +
94B TRP* 4.0 17.0 - - + -
165B ASP 3.0 8.2 + - - +
166B LEU* 3.7 11.5 - - + +
167B ILE* 2.9 28.6 + - - +
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Residues in contact with GLN 38 (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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36B PRO* 3.4 16.2 + - - +
37B VAL* 1.3 72.6 - - - +
39B VAL* 1.3 62.0 + - - +
40B THR* 4.1 3.6 + - - +
67B LYS 3.7 2.4 - - - +
68B TRP* 3.6 17.8 - - - +
69B ASN 4.7 1.7 + - - -
167B ILE* 3.5 38.1 - - - +
169B GLU* 4.3 11.6 - - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.0 8.5 - - + -
38B GLN* 1.3 75.6 - - - +
40B THR* 1.3 70.9 + - - +
41B CYS* 4.1 15.3 - - - -
66B GLN* 4.1 24.0 - - + +
67B LYS 3.3 10.3 - - - +
68B TRP* 4.2 3.8 - - + -
96B PRO* 3.7 17.3 - - + -
166B LEU* 3.5 31.6 - - + -
167B ILE 2.9 8.7 + - - +
168B PHE* 3.5 14.2 - - + +
169B GLU* 3.0 29.1 + - - +
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Residues in contact with THR 40 (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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38B GLN* 5.0 3.5 + - - +
39B VAL* 1.3 75.5 + - - +
41B CYS* 1.3 63.0 + - - +
42B ASN* 5.7 0.5 + - - -
65B ARG 3.7 0.7 - - - +
66B GLN* 3.4 3.5 - - - -
67B LYS* 2.8 48.5 + - + +
169B GLU* 3.3 9.2 + - - +
170B TRP 4.2 1.1 - - - +
171B GLN* 3.3 46.7 - - + +
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Residues in contact with CYS 41 (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 15.9 - - - -
40B THR* 1.3 81.5 - - - +
42B ASN* 1.3 63.5 + - - +
64B LEU* 5.0 2.7 - - + -
65B ARG 3.2 5.8 - - - +
66B GLN* 4.3 4.7 - - - -
98B LEU* 4.1 24.9 - - - -
156B LEU* 4.3 11.2 - - + -
168B PHE* 4.5 9.4 - - - -
169B GLU 2.9 13.7 + - - +
170B TRP* 3.4 11.1 - - + -
171B GLN* 3.0 23.4 + - - +
210B ILE* 4.2 20.2 - - + -
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Residues in contact with ASN 42 (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* 3.1 17.6 + - - +
40B THR 5.7 0.2 + - - -
41B CYS* 1.3 76.4 - - - +
43B ILE* 1.3 63.4 + - - +
63B PHE 3.9 0.2 - - - +
64B LEU* 4.3 0.5 - - - +
65B ARG* 2.7 82.3 + - - +
67B LYS* 4.1 8.7 - - - +
170B TRP* 4.3 2.2 - - - -
171B GLN* 3.0 35.9 + - - +
175B PRO* 3.1 19.1 - - + +
177B GLN* 3.2 5.2 + - - +
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Residues in contact with ILE 43 (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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42B ASN* 1.3 79.9 - - - +
44B PHE* 1.3 60.8 + - - +
45B ILE* 4.0 21.8 - - + -
62B ILE* 4.3 16.2 - - + -
63B PHE 3.3 7.2 - - - +
64B LEU* 4.0 21.8 - - + -
65B ARG* 4.2 0.7 - - - -
154B MET* 3.9 29.4 - - + -
156B LEU* 4.8 2.9 - - + -
170B TRP* 4.3 13.2 - - + -
175B PRO 2.9 7.3 + - - -
176B VAL* 3.5 29.1 - - + -
177B GLN* 2.9 33.2 + - - +
212B VAL* 4.5 4.5 - - + -
214B PHE* 4.5 3.8 - - + -
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Residues in contact with PHE 44 (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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201A HIS 5.9 0.4 - - - -
202A TYR* 3.7 33.4 - + + -
43B ILE* 1.3 73.0 - - - +
45B ILE* 1.3 61.6 + - - +
46B ASN* 3.4 34.8 + - + -
62B ILE* 3.2 7.2 - - - +
63B PHE* 2.9 51.4 + + + -
65B ARG* 3.7 23.2 - - - +
177B GLN* 3.5 23.6 - - + +
178B VAL 4.2 3.6 - - - -
179B ALA* 3.6 33.4 - - + -
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Residues in contact with ILE 45 (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* 4.0 15.3 - - + -
44B PHE* 1.3 73.8 - - - +
46B ASN* 1.3 60.4 + - - +
47B SER 3.6 26.2 - - - +
48B PHE* 4.1 16.4 - - + -
60B VAL* 4.9 3.1 - - + -
61B ASN 3.9 3.4 - - - +
62B ILE* 4.3 7.6 - - + -
154B MET* 5.4 2.0 - - + -
176B VAL* 3.9 13.5 - - + -
177B GLN 2.8 15.4 + - - +
178B VAL* 4.3 14.1 - - + -
179B ALA* 3.0 26.5 + - - +
182B LEU* 4.1 13.3 - - + +
189B LEU* 5.7 1.1 - - + -
214B PHE* 3.5 39.3 - - + -
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Residues in contact with ASN 46 (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* 5.7 0.2 - - - -
101A ALA* 2.9 31.7 + - - +
200A LYS* 5.6 2.4 + - - -
202A TYR* 5.2 2.6 + - - -
44B PHE* 3.4 26.8 + - + +
45B ILE* 1.3 73.6 - - - +
47B SER* 1.3 64.2 + - - +
61B ASN* 2.8 37.6 + - - +
63B PHE* 4.7 14.8 - - + -
131B ARG* 4.0 5.5 - - - +
179B ALA* 4.3 11.6 - - - +
182B LEU* 4.7 5.7 - - - +
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Residues in contact with SER 47 (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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104A LYS* 5.7 5.9 - - - +
45B ILE* 3.3 7.8 + - - +
46B ASN* 1.3 85.9 - - - +
48B PHE* 1.3 64.2 + - - +
49B GLY 5.2 0.2 + - - -
59B ARG* 5.2 1.0 + - - +
60B VAL* 3.3 5.1 - - - -
61B ASN* 3.0 42.7 + - - +
182B LEU* 4.3 10.1 - - - -
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Residues in contact with PHE 48 (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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45B ILE* 4.1 13.9 - - + -
47B SER* 1.3 77.9 + - - +
49B GLY* 1.3 62.5 + - - +
51B ILE* 4.0 19.3 - - + -
58B TYR* 3.7 33.7 - + - -
59B ARG 3.5 4.7 - - - -
60B VAL* 3.7 13.2 - - + -
152B CYS* 5.2 0.4 - - + -
182B LEU* 4.1 24.7 - - + +
183B THR 4.8 1.7 - - - +
184B LEU* 3.7 33.1 - - + +
189B LEU* 4.4 13.5 - - + -
214B PHE* 4.0 37.9 - + + -
216B LEU* 4.2 18.6 - - + -
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Residues in contact with GLY 49 (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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47B SER* 5.2 0.2 + - - -
48B PHE* 1.3 79.2 - - - +
50B SER* 1.3 70.6 + - - -
51B ILE* 3.0 12.3 + - - +
58B TYR* 3.8 1.7 - - - +
59B ARG* 2.9 30.9 + - - -
184B LEU* 5.2 2.2 - - - -
185B PRO* 6.5 0.7 - - - -
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Residues in contact with SER 50 (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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104A LYS* 5.5 1.4 + - - -
49B GLY* 1.3 73.7 - - - +
51B ILE* 1.3 59.6 + - - +
52B ALA* 3.1 13.6 + - - +
57B ASP* 3.5 8.8 - - - +
58B TYR* 3.5 4.9 - - - -
59B ARG* 3.7 36.9 + - - -
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Residues in contact with ILE 51 (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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48B PHE* 4.0 6.3 - - + -
49B GLY* 3.9 8.3 - - - +
50B SER* 1.3 73.5 - - - +
52B ALA* 1.3 58.9 + - - +
53B GLU* 4.0 11.3 - - - +
57B ASP 3.6 5.4 - - - +
58B TYR* 3.9 18.4 - - + -
140B MET* 3.8 23.3 - - + -
152B CYS* 5.6 0.4 - - - -
184B LEU* 3.5 32.8 - - + -
186B GLN* 4.6 11.9 + - - +
187B PHE* 3.6 39.2 - - + -
216B LEU* 3.9 21.1 - - + -
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Residues in contact with ALA 52 (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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50B SER 3.1 5.3 + - - +
51B ILE* 1.3 73.4 - - - +
53B GLU* 1.3 59.5 + - - +
54B THR* 4.3 8.5 - - - +
55B THR* 3.2 23.8 - - + +
56B MET* 2.9 22.7 + - - -
57B ASP* 2.9 24.2 + - - +
140B MET* 3.7 4.6 - - - +
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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