Contacts of the helix formed by residues 10 - 20 (chain D) in PDB entry 4RZR
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 TYR 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ASP* 1.3 79.7 - - + +
11D PHE* 1.3 59.8 + - - +
12D TYR 3.6 1.6 - - - -
13D ALA* 3.2 5.8 + - + -
14D GLN* 2.8 69.7 + - + +
17D GLU* 3.2 31.3 + - - -
45D THR* 4.4 2.2 - - - +
46D ALA 3.9 8.5 - - - +
47D ASN* 3.6 20.2 - - + -
48D TYR* 3.7 24.2 - + + -
51D ARG* 3.6 16.6 - - - +
139D THR* 4.6 4.0 + - - -
160D PRO* 5.4 2.7 - - + -
401D DCP 2.9 30.9 + - - -
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Residues in contact with PHE 11 (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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8D PHE* 3.7 29.8 - + + -
9D ASP 2.9 9.2 + - - -
10D TYR* 1.3 71.2 - - - +
12D TYR* 1.3 83.6 + + - +
14D GLN* 3.1 2.3 + - - -
15D VAL* 3.0 43.3 + - + +
81D TYR* 3.7 34.1 - - + -
84D VAL* 4.2 9.6 - - + -
85D SER* 4.1 11.7 - - - -
88D ILE* 4.6 3.6 - - + -
104D ILE* 4.0 17.7 - - + -
105D ASP* 3.8 24.7 - - + +
138D ILE* 4.7 10.1 - - + -
401D DCP 3.1 22.0 + - - +
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Residues in contact with TYR 12 (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 PHE* 1.3 101.9 - + - +
13D ALA* 1.3 63.4 + - - +
15D VAL* 3.3 3.3 + - - +
16D GLU* 3.2 24.9 + - - +
30D VAL* 4.0 8.5 - - + -
44D ALA* 4.2 9.4 - - + -
45D THR* 3.7 8.7 - - + +
76D MET* 3.8 26.7 - - + -
78D LYS* 3.2 27.3 - - - -
81D TYR* 3.4 46.4 - + + -
104D ILE* 3.9 19.4 - - + +
401D DCP 3.4 47.0 + - + -
5E 2JV 5.9 0.5 - - - -
6E G 4.5 1.9 + - - -
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Residues in contact with ALA 13 (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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10D TYR* 3.2 19.6 + - + +
12D TYR* 1.3 77.8 - - - +
14D GLN* 1.3 64.2 + - - +
16D GLU* 3.1 5.2 + - - +
17D GLU* 3.0 24.6 + - - +
28D VAL* 4.0 20.2 - - + +
30D VAL* 3.7 11.7 - - + -
45D THR* 3.6 12.9 - - + +
46D ALA 4.3 0.2 - - - -
47D ASN* 3.9 20.9 - - + +
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Residues in contact with GLN 14 (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 ASP* 2.7 29.2 + - - +
10D TYR* 2.8 45.6 + - + +
11D PHE* 3.1 3.7 + - - +
13D ALA* 1.3 77.8 - - - +
15D VAL* 1.3 61.8 + - - +
17D GLU* 3.2 6.9 + - + +
18D VAL* 3.0 24.6 + - + +
137D LYS 3.9 4.0 - - - +
138D ILE* 3.6 22.3 - - + +
139D THR* 2.9 55.6 + - - +
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Residues in contact with VAL 15 (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 PHE* 3.0 50.5 + - + +
12D TYR 3.7 6.3 - - - +
13D ALA 3.3 0.2 - - - -
14D GLN* 1.3 75.6 - - - +
16D GLU* 1.3 64.1 + - - +
18D VAL* 3.1 10.7 + - + +
19D LEU* 3.0 41.0 + - + +
80D VAL* 4.3 1.8 - - + -
81D TYR* 3.7 24.5 - - + -
84D VAL* 4.1 24.7 - - + -
138D ILE* 4.4 7.0 - - + -
405D GOL 5.3 0.2 - - - +
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Residues in contact with GLU 16 (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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12D TYR 3.2 14.1 + - - +
13D ALA* 3.1 10.0 + - - +
15D VAL* 1.3 78.6 - - - +
17D GLU* 1.3 55.6 + - - +
19D LEU* 3.5 4.8 + - - +
20D ASN* 2.9 31.4 + - - +
23D LEU* 3.7 5.3 - - + +
28D VAL* 4.8 1.1 - - + -
30D VAL* 4.1 7.9 - - + -
74D LEU* 3.7 34.4 - - + +
75D PRO 4.1 5.4 - - - +
77D ARG* 2.9 40.7 + - - -
81D TYR* 2.5 30.7 + - - +
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Residues in contact with GLU 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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10D TYR* 3.2 35.3 + - - -
13D ALA 3.0 14.8 + - - +
14D GLN* 3.5 9.1 - - + +
16D GLU* 1.3 74.8 - - - +
18D VAL* 1.3 65.0 + - + +
20D ASN 3.1 7.3 - - - +
21D PRO* 3.1 29.5 - - - +
23D LEU* 4.3 16.2 - - + -
24D LYS* 3.4 38.5 + - + +
28D VAL* 4.1 6.2 - - + +
47D ASN* 2.9 31.5 + - - +
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Residues in contact with VAL 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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14D GLN* 3.0 19.2 + - + +
15D VAL* 3.1 9.6 + - + +
17D GLU* 1.3 77.7 - - - +
19D LEU* 1.3 70.3 + - + +
21D PRO* 3.6 11.1 - - - +
24D LYS* 5.8 1.1 - - - +
136D GLU 4.0 12.6 - - - +
137D LYS* 3.5 38.4 - - + +
138D ILE* 3.8 15.7 - - + -
405D GOL 5.7 3.4 - - - +
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Residues in contact with LEU 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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15D VAL* 3.0 26.8 + - + +
16D GLU* 3.9 6.7 - - - +
18D VAL* 1.3 81.3 - - + +
20D ASN* 1.3 60.4 + - + +
21D PRO* 3.8 4.1 - - - +
77D ARG* 3.4 29.6 - - - +
80D VAL* 3.6 24.7 - - + -
405D GOL 3.9 27.1 - - - +
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Residues in contact with ASN 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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16D GLU 2.9 13.1 + - - +
17D GLU 3.1 6.2 - - - +
19D LEU* 1.3 78.6 - - - +
21D PRO* 1.3 65.4 - - - +
22D SER* 2.9 24.4 + - - -
23D LEU* 3.0 39.8 + - + +
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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