Contacts of the strand formed by residues 39 - 47 (chain D) in PDB entry 1U1C
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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D MET* 1.3 71.7 - - - +
40D LYS* 1.3 65.7 + - + +
55D ALA* 3.7 0.7 - - - -
56D GLU* 2.7 55.8 + - + +
57D LEU* 5.3 0.9 - - - +
58D ASP 5.1 6.4 + - - -
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Residues in contact with LYS 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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39D ASP* 1.3 79.1 - - + +
41D PRO* 1.3 72.7 - - - +
42D VAL* 3.7 12.4 + - + +
54D ARG 3.4 10.9 - - - +
55D ALA* 3.5 4.7 - - - -
56D GLU* 4.0 24.6 + - + +
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Residues in contact with PRO 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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35D ALA 3.5 26.0 - - - +
36D ALA* 4.1 15.0 - - + +
38D MET 4.3 2.9 - - - +
39D ASP 4.1 1.3 - - - -
40D LYS* 1.3 89.3 - - - +
42D VAL* 1.3 64.2 + - - +
53D TRP* 3.7 25.7 - - + -
54D ARG 3.6 4.9 - - - +
55D ALA* 4.6 1.6 - - + -
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Residues in contact with VAL 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 LYS* 4.4 14.6 - - + +
41D PRO* 1.3 79.7 - - - +
43D LYS* 1.3 74.6 + - - +
44D LEU* 3.6 9.6 + - + -
53D TRP* 3.4 7.4 - - - -
54D ARG* 2.8 68.2 + - + +
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Residues in contact with LYS 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 VAL* 1.3 81.5 - - - +
44D LEU* 1.3 64.3 + - - +
45D ALA* 4.6 4.0 - - - +
46D SER* 3.8 36.0 + - - +
51D THR* 4.6 8.0 - - + +
52D THR 4.4 1.8 - - - +
53D TRP* 3.4 47.1 - - + +
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Residues in contact with LEU 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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11D LEU* 3.7 25.1 - - + -
15D ASP* 3.9 27.1 - - + +
16D LEU* 5.4 0.4 - - + -
42D VAL* 4.3 6.1 - - + +
43D LYS* 1.3 81.1 - - - +
45D ALA* 1.3 61.7 + - - +
52D THR* 2.9 20.4 + - + +
54D ARG* 3.8 52.7 - - + +
63D ILE* 3.8 20.0 - - + -
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Residues in contact with ALA 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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9D LEU 3.7 22.4 - - - +
10D GLY 3.7 15.7 - - - +
11D LEU* 4.2 8.7 - - + +
43D LYS* 4.6 6.8 - - - +
44D LEU* 1.3 82.2 - - - +
46D SER* 1.3 61.3 + - - +
47D HIS* 3.9 11.7 - - + +
50D PHE 3.7 2.0 - - - +
51D THR* 3.6 2.4 - - - +
52D THR* 2.9 28.8 + - - +
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Residues in contact with SER 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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29C ASP* 5.1 4.3 - - - +
43D LYS* 3.8 26.7 + - - +
45D ALA* 1.3 75.0 - - - +
47D HIS* 1.3 72.8 + - - +
48D ARG 5.5 2.4 + - - -
50D PHE 3.5 4.2 - - - -
51D THR* 3.2 21.7 + - - +
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Residues in contact with HIS 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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29C ASP* 4.5 3.1 - - - -
8D HIS 3.5 19.1 - - - +
9D LEU 3.4 19.4 + - - +
10D GLY* 4.1 13.2 - - - -
45D ALA* 3.9 19.1 - - + +
46D SER* 1.3 82.8 + - - +
48D ARG* 1.3 63.5 + - + +
49D GLU 3.1 0.2 + - - -
50D PHE* 2.8 42.5 + - - +
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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
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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