Contacts of the strand formed by residues 25 - 33 (chain D) in PDB entry 1RHP
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 THR 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.1 33.2 + - - +
48A GLY* 3.7 13.7 - - - -
49A ARG* 3.4 34.4 + - - +
29C VAL 3.6 1.4 - - - +
30C ILE* 3.5 3.0 - - + -
31C LYS* 2.8 37.2 + - - +
24D ILE* 1.3 74.3 + - - +
26D SER* 1.3 58.9 + - - +
44D THR 2.8 14.0 + - - -
45D LEU 4.5 6.9 + - - -
46D LYS* 4.6 12.6 + - - +
67D LEU* 3.6 4.5 - - - +
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Residues in contact with SER 26 (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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48A GLY* 4.7 10.5 - - - -
28C GLU* 3.4 32.6 + - - +
29C VAL 3.2 8.9 + - - -
30C ILE* 4.4 6.7 - - - +
24D ILE* 3.1 18.7 - - - +
25D THR* 1.3 83.5 - - - +
27D LEU* 1.3 62.6 + - - +
28D GLU* 4.7 0.9 + - - +
42D ILE 4.3 1.8 - - - -
43D ALA* 3.6 0.3 - - - -
44D THR* 3.4 31.0 + - - -
67D LEU* 4.9 0.4 - - - -
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Residues in contact with LEU 27 (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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27C LEU* 3.9 1.4 - - - +
28C GLU* 3.6 0.9 - - - -
29C VAL* 3.1 29.5 + - + +
24D ILE* 4.5 0.2 - - + -
26D SER* 1.3 78.1 + - - +
28D GLU* 1.3 65.1 + - - +
29D VAL* 4.2 14.7 + - + +
41D LEU* 4.6 9.2 - - + -
42D ILE 3.4 7.6 - - - -
43D ALA* 4.1 17.0 - - + +
53D LEU* 3.8 24.7 - - + -
60D TYR* 4.7 6.3 - - + -
63D ILE* 3.6 21.8 - - + -
64D ILE* 3.8 33.9 - - + -
67D LEU* 3.9 14.1 - - + -
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Residues in contact with GLU 28 (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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26C SER* 3.6 23.0 + - - -
27C LEU 3.1 10.5 - - - +
28C GLU* 4.0 25.2 - - + +
11D LEU* 5.4 2.8 - - - +
26D SER* 4.7 1.0 + - - +
27D LEU* 1.3 73.4 - - - +
29D VAL* 1.3 61.5 + - - +
30D ILE* 3.9 25.0 - - + +
40D GLN 3.5 1.4 - - - +
41D LEU* 3.2 7.8 - - - -
42D ILE* 3.0 48.3 + - + +
50D LYS* 5.2 7.5 + - - +
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Residues in contact with VAL 29 (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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26C SER* 3.1 6.1 - - - -
27C LEU* 2.9 47.5 + - + +
64C ILE* 5.2 5.8 - - + -
67C LEU* 3.7 34.8 - - + +
68C LEU* 4.0 23.6 - - + -
27D LEU* 4.2 22.4 - - + +
28D GLU* 1.3 78.8 - - - +
30D ILE* 1.3 61.7 + - - +
39D ALA* 5.8 0.2 - - + -
40D GLN 3.3 6.5 - - - +
41D LEU* 4.2 11.2 - - + -
64D ILE* 5.0 8.5 - - + -
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Residues in contact with ILE 30 (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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25C THR* 3.4 16.4 - - + +
26C SER* 4.2 9.2 - - - +
67C LEU* 4.7 0.9 - - - -
11D LEU* 4.9 4.9 - - + -
28D GLU* 3.9 25.6 - - + +
29D VAL* 1.3 79.3 - - - +
31D LYS* 1.4 64.5 + - - +
35D HIS* 3.9 23.9 + - + +
38D THR 4.5 0.3 - - - +
39D ALA* 3.5 3.6 - - - +
40D GLN* 3.1 44.8 + - + +
42D ILE* 3.5 31.9 - - + -
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Residues in contact with LYS 31 (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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24C ILE 4.0 11.4 - - - +
25C THR* 3.0 28.1 + - - +
46C LYS* 3.1 42.8 - - - +
66C LYS 5.2 2.2 - - - +
67C LEU* 4.2 35.1 - - + +
70C SER* 5.9 0.7 - - - +
30D ILE* 1.4 70.7 - - - +
32D ALA* 1.3 67.9 + - - +
33D GLY* 4.8 7.3 - - - -
34D PRO* 5.4 4.0 - - - +
35D HIS* 2.5 47.9 + - + -
38D THR 4.6 0.2 - - - +
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Residues in contact with ALA 32 (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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67C LEU 5.0 0.4 + - - -
70C SER* 3.6 29.7 + - - +
31D LYS* 1.3 94.2 - - - +
33D GLY* 1.3 58.3 + - - +
36D CYS 3.7 5.8 - - - -
37D PRO* 3.5 27.4 - - + +
38D THR 3.9 7.4 - - - -
39D ALA* 4.3 3.2 - - - +
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Residues in contact with GLY 33 (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 LYS* 3.6 7.1 + - - -
32D ALA* 1.3 76.4 - - - +
34D PRO* 1.3 70.4 - - - +
35D HIS* 3.1 8.8 - - - -
36D CYS 2.7 30.5 + - - +
37D PRO* 3.7 3.6 - - - +
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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