Contacts of the strand formed by residues 37 - 52 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ARG* 3.7 9.2 - - - +
30D PRO* 3.4 45.1 - - + +
31D ASN* 5.8 2.0 - - - +
35D PRO 3.7 0.4 + - - -
36D PRO* 1.3 70.1 - - - +
38D GLN* 1.3 61.6 + - - +
39D VAL* 3.6 19.5 + - + -
68D TRP* 4.0 18.8 - - + -
69D ASN 4.9 4.0 - - - +
94D TRP* 4.0 17.0 - - + -
165D ASP 3.0 8.5 + - - +
166D LEU* 3.7 10.7 - - + +
167D ILE* 2.9 29.5 + - - +
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Residues in contact with GLN 38 (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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36D PRO* 3.4 16.0 + - - +
37D VAL* 1.3 72.2 - - - +
39D VAL* 1.3 62.9 + - - +
40D THR* 4.1 3.0 + - - +
67D LYS 3.7 2.6 - - - +
68D TRP* 3.6 17.7 - - - +
69D ASN 4.7 1.6 + - - -
167D ILE* 3.5 37.7 - - - +
169D GLU* 4.3 12.4 - - + +
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Residues in contact with VAL 39 (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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37D VAL* 4.0 9.0 - - + -
38D GLN* 1.3 75.8 - - - +
40D THR* 1.3 70.9 + - - +
41D CYS* 4.1 14.1 - - - -
66D GLN* 4.1 24.0 - - + +
67D LYS 3.3 10.5 - - - +
68D TRP* 4.2 3.8 - - + -
96D PRO* 3.7 17.7 - - + -
166D LEU* 3.5 30.5 - - + -
167D ILE 2.8 11.6 + - - +
168D PHE* 3.5 10.7 - - + -
169D GLU* 3.0 29.9 + - - +
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Residues in contact with THR 40 (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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38D GLN* 4.1 3.3 + - - +
39D VAL* 1.3 74.3 + - - +
41D CYS* 1.3 63.4 + - - +
42D ASN* 5.6 0.5 + - - -
65D ARG 3.7 0.3 - - - +
66D GLN* 3.4 3.8 - - - -
67D LYS* 2.8 49.3 + - + +
169D GLU* 3.3 8.8 + - - +
170D TRP 4.2 1.1 - - - +
171D GLN* 3.4 45.3 - - + +
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Residues in contact with CYS 41 (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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39D VAL* 4.1 17.0 - - - -
40D THR* 1.3 79.2 - - - +
42D ASN* 1.3 64.4 + - - +
64D LEU* 5.0 2.2 - - + -
65D ARG 3.3 6.3 - - - +
66D GLN* 4.3 4.9 - - - -
98D LEU* 4.1 24.0 - - - -
156D LEU* 4.3 11.9 - - + -
168D PHE* 4.5 9.2 - - - -
169D GLU 2.9 15.4 + - - +
170D TRP* 3.4 10.4 - - + -
171D GLN* 3.0 22.6 + - - -
175D PRO* 4.4 0.2 - - - +
210D ILE* 4.2 20.2 - - + -
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Residues in contact with ASN 42 (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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203C ASN* 3.0 16.8 + - - +
40D THR 5.6 0.4 + - - -
41D CYS* 1.3 75.4 - - - +
43D ILE* 1.3 63.4 + - - +
64D LEU* 4.3 0.3 - - - +
65D ARG* 2.7 84.2 + - - +
67D LYS* 4.1 8.7 - - - +
170D TRP* 4.3 2.2 - - - -
171D GLN* 3.0 33.0 + - - +
175D PRO* 3.1 22.7 - - + +
177D GLN* 3.2 4.2 + - - +
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Residues in contact with ILE 43 (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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42D ASN* 1.3 80.6 - - - +
44D PHE* 1.3 60.6 + - - +
45D ILE* 4.0 22.2 - - + -
62D ILE* 4.3 15.5 - - + -
63D PHE 3.3 8.1 - - - +
64D LEU* 4.0 21.3 - - + -
65D ARG* 4.2 0.7 - - - -
100D PHE* 5.9 0.2 - - + -
154D MET* 3.9 28.9 - - + -
156D LEU* 4.8 2.9 - - + -
170D TRP* 4.3 14.4 - - + -
175D PRO 2.9 6.7 + - - -
176D VAL* 3.5 27.5 - - + -
177D GLN* 2.9 32.9 + - - +
212D VAL* 4.6 4.7 - - + -
214D PHE* 4.5 3.8 - - + -
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Residues in contact with PHE 44 (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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201C HIS 5.9 0.7 - - - -
202C TYR* 3.7 35.7 - + + -
43D ILE* 1.3 72.8 - - - +
45D ILE* 1.3 61.5 + - - +
46D ASN* 3.4 34.9 + - + -
62D ILE* 3.2 7.6 - - - -
63D PHE* 2.9 52.5 + + + -
65D ARG* 3.7 23.7 - - - +
177D GLN* 3.5 23.8 - - + +
178D VAL 4.2 2.9 - - - -
179D ALA* 3.6 34.1 - - + -
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Residues in contact with ILE 45 (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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43D ILE* 4.0 15.0 - - + -
44D PHE* 1.3 74.0 - - - +
46D ASN* 1.3 61.1 + - - +
47D SER 3.6 26.0 - - - +
48D PHE* 4.1 17.0 - - + -
60D VAL* 4.9 2.9 - - + -
61D ASN 3.9 2.9 - - - +
62D ILE* 4.3 7.4 - - + -
154D MET* 5.4 1.8 - - + -
176D VAL* 3.9 13.5 - - + -
177D GLN 2.8 15.6 + - - +
178D VAL* 4.3 13.5 - - + -
179D ALA* 3.0 25.3 + - - +
182D LEU* 4.1 12.3 - - + +
189D LEU* 5.7 0.7 - - + -
214D PHE* 3.5 38.6 - - + -
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Residues in contact with ASN 46 (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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99C PHE* 5.6 0.2 - - - -
101C ALA* 2.9 32.1 + - - +
200C LYS* 5.6 2.3 + - - -
202C TYR* 5.2 2.8 + - - -
44D PHE* 3.4 26.5 + - + +
45D ILE* 1.3 73.6 - - - +
47D SER* 1.3 64.3 + - - +
61D ASN* 2.8 37.6 + - - +
63D PHE* 4.7 15.4 - - + -
131D ARG* 4.0 5.3 - - - +
179D ALA* 4.3 12.4 - - - +
182D LEU* 4.7 5.1 - - - +
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Residues in contact with SER 47 (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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104C LYS* 5.7 5.9 - - - +
45D ILE* 3.3 8.9 - - - +
46D ASN* 1.3 85.0 - - - +
48D PHE* 1.3 64.9 + - - +
49D GLY 5.2 0.3 + - - -
59D ARG* 5.2 1.0 + - - +
60D VAL* 3.3 5.4 - - - -
61D ASN* 3.0 44.5 + - - +
182D LEU* 4.3 10.1 - - - -
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Residues in contact with PHE 48 (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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45D ILE* 4.1 13.9 - - + -
47D SER* 1.3 78.1 + - - +
49D GLY* 1.3 61.1 + - - +
51D ILE* 4.0 18.8 - - + -
58D TYR* 3.7 28.0 - + - -
59D ARG 3.5 5.2 - - - -
60D VAL* 3.7 18.2 - - + -
152D CYS* 5.2 0.9 - - + -
182D LEU* 4.1 24.2 - - + +
183D THR 4.8 2.1 - - - +
184D LEU* 3.7 34.6 - - + +
189D LEU* 4.4 13.7 - - + -
214D PHE* 4.0 37.0 - + + -
216D LEU* 4.2 17.9 - - + -
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Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D SER* 5.2 0.6 + - - -
48D PHE* 1.3 79.0 - - - +
50D SER* 1.3 70.9 + - - -
51D ILE* 3.1 14.0 + - - +
58D TYR* 3.9 0.5 - - - +
59D ARG* 2.9 29.7 + - - -
184D LEU* 5.2 1.8 - - - -
185D PRO* 6.5 0.4 - - - -
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Residues in contact with SER 50 (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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104C LYS* 5.5 2.4 + - - -
49D GLY* 1.3 72.3 - - - +
51D ILE* 1.3 60.0 + - - +
52D ALA* 3.1 12.8 + - - +
57D ASP* 3.5 10.0 - - - +
58D TYR* 3.6 4.7 - - - -
59D ARG* 3.7 36.6 + - - -
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Residues in contact with ILE 51 (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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48D PHE* 4.0 7.0 - - + -
49D GLY* 3.9 8.7 - - - +
50D SER* 1.3 74.2 - - - +
52D ALA* 1.3 59.2 + - - +
53D GLU* 4.0 10.7 - - - +
57D ASP 3.6 5.2 - - - +
58D TYR* 3.9 17.9 - - + -
140D MET* 3.8 23.8 - - + -
152D CYS* 5.6 0.4 - - - -
184D LEU* 3.5 32.8 - - + -
186D GLN* 4.6 11.7 + - - +
187D PHE* 3.6 38.5 - - + -
216D LEU* 3.9 20.0 - - + -
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Residues in contact with ALA 52 (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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50D SER 3.1 5.6 + - - +
51D ILE* 1.3 72.0 - - - +
53D GLU* 1.3 60.7 + - - +
54D THR* 4.3 8.7 - - - +
55D THR* 3.2 23.1 - - - +
56D MET* 2.9 22.5 + - - -
57D ASP* 2.9 24.6 + - - +
140D MET* 3.7 4.7 - - - +
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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