Contacts of the strand formed by residues 35 - 44 (chain D) in PDB entry 1D1T
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 35 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PRO* 3.5 2.4 - - + +
32D LYS* 3.0 31.7 + - - +
33D THR 3.2 10.2 - - - +
34D LYS* 1.3 75.9 - - - +
36D VAL* 1.3 64.3 + - - +
77D GLY 2.8 25.5 + - - -
80D VAL* 3.4 4.3 - - - +
123D LEU* 3.7 12.7 - - + +
125D ASP* 4.4 7.1 + - - +
129D ARG* 2.8 45.9 + - - -
151D VAL* 3.4 11.6 - - + +
152D VAL 3.1 11.7 - - - +
153D ASP* 3.7 18.9 - - - +
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Residues in contact with VAL 36 (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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31D PRO* 4.3 0.2 - - - -
35D GLU* 1.3 80.6 - - - +
37D ARG* 1.3 60.0 + - - +
38D ILE* 3.8 13.8 + - + -
73D VAL* 3.5 34.3 - - + -
75D SER 3.9 4.3 - - - +
76D ILE* 4.4 1.3 - - + -
80D VAL* 4.2 11.2 - - + -
83D VAL* 3.9 22.7 - - + -
150D THR 3.7 0.5 - - - +
151D VAL* 3.1 5.2 - - - -
152D VAL* 2.8 33.0 + - + +
154D GLU* 4.2 10.8 - - + -
157D VAL* 3.8 28.9 - - + -
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Residues in contact with ARG 37 (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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2D THR 2.8 21.0 + - - -
3D ALA* 4.4 1.2 - - - +
4D GLY 4.4 0.8 - - - +
5D LYS 2.8 29.2 + - - +
7D ILE* 3.4 19.3 - - - +
28D VAL* 2.7 39.1 + - + -
29D ALA 3.9 1.1 - - - -
30D PRO* 3.5 14.1 - - - -
31D PRO* 3.7 17.3 - - + +
36D VAL* 1.3 71.4 - - - +
38D ILE* 1.3 56.9 + - - +
73D VAL* 3.7 3.1 - - - +
74D GLU* 2.7 66.4 + - - +
75D SER* 2.9 15.8 + - - +
149D TYR* 4.6 9.6 - - + -
150D THR 3.3 11.2 - - - +
151D VAL* 3.9 17.7 - - + +
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Residues in contact with ILE 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 VAL* 4.1 15.5 - - + +
37D ARG* 1.3 78.7 - - - +
39D LYS* 1.3 68.6 + - - +
40D ILE* 3.7 9.2 + - + +
71D GLY* 3.7 9.4 - - - -
72D ILE 3.4 24.7 - - - +
73D VAL* 4.7 0.9 - - - -
89D VAL* 3.8 23.8 - - + -
91D PRO* 4.4 18.4 - - + -
149D TYR* 3.0 11.8 - - - +
150D THR* 2.7 43.4 + - + +
152D VAL* 3.6 32.1 - - + -
157D VAL* 4.7 5.8 - - + -
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Residues in contact with LYS 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 ARG 4.3 0.2 + - - -
38D ILE* 1.3 71.8 - - - +
40D ILE* 1.3 67.1 + - - +
41D LEU* 3.5 20.4 + - + +
71D GLY* 3.2 3.6 - - - -
72D ILE* 2.8 45.1 + - + +
74D GLU* 4.6 4.4 - - + +
148D GLU* 3.4 7.4 - - + +
149D TYR* 3.4 39.6 + - + +
374D PHE* 6.2 2.7 - - - -
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Residues in contact with ILE 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 ILE* 4.4 16.8 - - + +
39D LYS* 1.3 77.5 - - - +
41D LEU* 1.3 64.2 + - - +
42D ALA 3.9 18.6 - - - +
43D THR* 4.3 0.4 - - - -
69D ALA* 4.2 18.6 - - + -
70D THR 4.1 3.6 - - - +
71D GLY* 5.0 0.7 - - - -
91D PRO* 4.8 6.1 - - + -
145D THR* 3.7 25.6 - - + +
147D THR* 3.1 25.8 - - + +
148D GLU* 2.7 13.7 + - - +
149D TYR* 4.7 1.6 - - - +
150D THR* 4.5 13.0 - - + -
374D PHE* 3.1 44.7 - - + +
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Residues in contact with LEU 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 LYS* 3.5 24.4 + - + +
40D ILE* 1.3 78.8 - - - +
42D ALA* 1.3 64.3 + - - +
70D THR* 2.9 14.0 + - + +
71D GLY* 4.3 3.6 - - - +
72D ILE* 3.6 36.1 - - + -
88D LYS* 5.0 6.1 - - - +
166D PRO* 4.0 29.4 - - + -
373D THR* 3.8 3.8 - - - +
374D PHE* 3.2 31.4 + - + +
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Residues in contact with ALA 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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40D ILE* 3.8 2.8 - - - +
41D LEU* 1.3 82.5 - - - +
43D THR* 1.3 60.8 + - - +
69D ALA* 3.1 4.7 - - - +
70D THR 2.9 29.0 + - - -
166D PRO* 3.5 27.6 - - + +
167D GLU* 3.7 19.3 - - + +
170D CYS* 3.8 3.6 - - - +
371D VAL* 4.0 6.7 - - + -
372D LEU 3.3 11.4 - - - +
373D THR* 4.8 2.2 - - + -
374D PHE* 4.9 0.2 - - - -
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Residues in contact with THR 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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40D ILE* 4.3 0.9 - - - -
42D ALA* 1.3 75.7 - - - +
44D GLY* 1.3 61.0 + - - +
68D GLU 2.6 15.0 + - - -
69D ALA* 3.7 5.2 - - - +
145D THR* 2.6 43.9 + - - +
146D PHE* 3.6 20.4 - - + -
170D CYS* 4.6 1.8 - - - -
371D VAL* 4.4 2.2 - - - +
372D LEU* 2.8 51.8 + - + +
374D PHE* 4.1 13.5 - - + -
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Residues in contact with GLY 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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43D THR* 1.3 83.0 + - - +
45D ILE* 1.3 63.2 + - - -
46D CYS 3.6 2.8 + - - -
49D ASP* 4.2 1.9 - - - +
67D HIS 5.3 0.2 + - - -
68D GLU* 2.9 41.3 + - - +
146D PHE* 3.8 9.9 - - - -
170D CYS* 4.3 4.0 - - - -
171D LEU* 4.8 1.1 - - - -
369D ARG* 5.0 0.2 - - - -
370D THR 3.4 8.5 - - - -
371D VAL* 4.3 9.4 - - - -
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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