Contacts of the strand formed by residues 16 - 24 (chain D) in PDB entry 1C04
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 ALA 16 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 3.3 27.1 - - + +
12D ASP* 4.5 4.9 - - - +
14D SER* 3.3 4.6 + - - +
15D GLY* 1.3 79.5 + - - +
17D ARG* 1.3 60.6 + - - +
19D VAL* 4.7 1.8 - - + -
43D VAL* 4.1 11.7 - - + -
45D ASP 3.8 4.7 - - - -
46D ALA* 4.2 4.5 - - - -
52D VAL* 4.0 14.6 - - + +
86D ILE* 3.4 33.9 - - + -
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Residues in contact with ARG 17 (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 LYS* 3.9 6.6 - - - +
10D VAL* 3.3 21.6 + - - +
15D GLY 3.6 11.4 - - - +
16D ALA* 1.3 77.5 - - - +
18D GLU* 1.3 60.3 + - + +
45D ASP* 2.8 57.3 + - + +
46D ALA* 3.3 17.2 + - - -
47D THR* 3.6 30.0 - - + +
48D PRO* 4.3 8.7 - - - +
54D LYS* 5.1 3.4 - - - +
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Residues in contact with GLU 18 (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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7D ARG* 3.9 23.1 + - + +
8D LEU 3.3 13.7 - - - +
9D LYS* 3.8 26.7 + - - +
10D VAL* 3.9 1.7 - - - +
16D ALA 3.8 0.4 - - - -
17D ARG* 1.3 80.2 - - + +
19D VAL* 1.3 69.4 + - - +
43D VAL* 3.7 0.7 - - - +
44D LYS* 2.8 61.6 + - + +
45D ASP* 3.3 18.5 + - + +
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Residues in contact with VAL 19 (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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6D SER 3.7 0.5 - - - +
7D ARG* 3.2 7.6 - - - +
8D LEU* 2.9 46.9 + - + +
10D VAL* 4.1 12.3 - - + -
16D ALA* 4.7 1.3 - - + -
18D GLU* 1.3 80.0 - - - +
20D LEU* 1.3 60.4 + - - +
41D ALA* 3.7 17.3 - - + -
42D THR 3.2 13.0 - - - +
43D VAL* 4.0 12.8 - - + -
44D LYS* 4.1 2.7 - - - +
58D VAL* 4.3 19.1 - - + -
60D ALA* 5.3 1.3 - - + -
84D CYS* 3.7 29.2 - - - -
86D ILE* 4.7 5.6 - - + -
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Residues in contact with LEU 20 (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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5D GLU* 3.1 47.1 - - + +
6D SER 3.4 0.7 - - - -
7D ARG* 3.8 22.7 - - + +
19D VAL* 1.3 73.4 - - - +
21D VAL* 1.3 67.0 + - - +
22D ILE* 3.5 2.0 + - + +
41D ALA* 3.2 3.6 - - - +
42D THR* 2.9 45.1 + - - +
44D LYS* 4.9 14.6 - - + -
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Residues in contact with VAL 21 (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 ILE* 4.0 12.1 - - + -
3D GLN* 3.3 30.7 - - - +
4D GLN* 3.5 2.8 - - - +
5D GLU* 2.7 29.1 + - - +
6D SER* 2.9 19.1 + - - +
8D LEU* 3.7 30.7 - - + -
20D LEU* 1.3 73.8 - - - +
22D ILE* 1.3 61.6 + - - +
23D LYS 3.8 22.4 - - - +
24D VAL* 4.7 4.0 - - + -
39D VAL* 4.2 16.2 - - + -
40D VAL 3.9 4.3 - - - +
41D ALA* 4.1 1.8 - - + -
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Residues in contact with ILE 22 (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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4D GLN* 3.6 21.0 - - - +
20D LEU* 4.1 4.9 - - + +
21D VAL* 1.3 76.6 - - - +
23D LYS* 1.3 78.1 + - + +
40D VAL* 2.8 25.1 + - + +
41D ALA* 4.0 9.2 - - - -
42D THR* 3.4 34.8 - - + +
57D VAL* 4.4 9.2 - - + -
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Residues in contact with LYS 23 (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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4D GLN* 5.5 1.3 - - - +
21D VAL* 3.8 4.4 - - - +
22D ILE* 1.3 93.2 - - + +
24D VAL* 1.3 66.3 + - - +
25D LEU* 4.1 17.5 - - + -
39D VAL* 3.4 6.8 - - - +
40D VAL* 3.0 49.6 + - + -
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Residues in contact with VAL 24 (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 ILE 4.7 2.7 - - - +
3D GLN* 5.0 1.3 - - - -
4D GLN 5.6 0.7 - - - +
21D VAL* 4.7 7.4 - - + -
23D LYS* 1.3 80.4 - - - +
25D LEU* 1.3 74.7 + - - +
26D GLY 4.0 0.2 + - - -
27D GLY 4.9 2.4 + - - +
30D ARG* 4.0 39.4 + - + +
31D ARG* 3.6 26.9 - - - +
32D TYR 3.9 15.9 - - - +
33D ALA* 3.9 26.7 - - + +
37D ASP* 4.6 2.9 - - + -
38D VAL 3.9 7.9 - - - +
39D VAL* 4.3 5.4 - - + -
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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