Contacts of the strand formed by residues 37 - 46 (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 PRO 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C SER* 4.5 6.6 - - - -
10D CYS* 4.7 3.1 - - - -
32D ALA* 3.5 15.3 - - + +
33D GLY 3.7 5.6 - - - +
34D PRO 6.0 0.4 - - - -
36D CYS* 1.3 83.3 - - + +
38D THR* 1.3 57.9 + - + +
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Residues in contact with THR 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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70C SER* 5.1 4.3 - - - -
10D CYS* 4.6 1.6 - - + -
12D CYS* 6.5 0.2 - - + -
30D ILE 4.5 0.7 - - - +
31D LYS 4.6 0.5 - - - +
32D ALA* 3.9 8.4 - - - -
36D CYS* 3.2 34.7 - - - +
37D PRO* 1.3 80.6 - - + +
39D ALA* 1.3 76.6 + - - +
40D GLN* 3.8 9.7 + - + +
55D LEU* 3.7 15.8 - - - +
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Residues in contact with ALA 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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67C LEU 3.5 24.7 - - - +
68C LEU* 4.4 9.0 - - + +
70C SER* 4.4 6.6 - - - -
29D VAL* 5.8 0.4 - - + -
30D ILE 3.5 9.9 - - - +
32D ALA* 4.1 8.2 - - - +
38D THR* 1.3 90.4 + - - +
40D GLN* 1.3 62.0 + - - +
41D LEU* 4.9 1.8 - - + -
55D LEU* 3.9 33.7 - - + +
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Residues in contact with GLN 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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9D GLN 5.3 0.2 + - - -
10D CYS* 4.4 0.2 - - - +
11D LEU* 2.9 40.3 + - - +
12D CYS* 3.4 26.0 + - + -
28D GLU 3.5 1.1 - - - +
29D VAL* 3.3 6.1 - - - +
30D ILE* 3.1 50.8 + - + +
35D HIS* 3.4 31.9 + - - -
36D CYS* 3.7 21.0 - - - +
38D THR* 4.1 7.2 + - + +
39D ALA* 1.3 77.6 - - - +
41D LEU* 1.3 65.6 + - - +
42D ILE* 4.2 1.6 - - + +
53D LEU 5.8 0.2 - - - -
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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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68C LEU* 3.4 26.9 - - + -
12D CYS* 4.9 1.4 - - - -
27D LEU* 4.6 10.1 - - + -
28D GLU 3.2 5.6 - - - +
29D VAL* 4.2 14.1 - - + -
39D ALA 4.9 0.7 - - - -
40D GLN* 1.3 83.4 - - - +
42D ILE* 1.3 58.3 + - - +
43D ALA 4.2 0.4 + - - -
52D CYS* 3.0 6.6 - - - +
53D LEU* 2.9 54.2 + - + +
54D ASP 5.1 0.9 - - - +
55D LEU* 4.4 20.6 - - + -
60D TYR* 3.7 43.5 - - + -
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Residues in contact with ILE 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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7B ASP 5.3 1.3 - - - +
11D LEU* 3.2 36.1 - - + -
12D CYS* 3.8 21.1 - - - -
26D SER* 4.0 1.0 - - - +
27D LEU* 3.4 5.4 + - - +
28D GLU* 3.0 43.0 + - + +
30D ILE* 3.5 26.2 - - + -
40D GLN* 4.5 0.9 - - + +
41D LEU* 1.3 75.7 - - - +
43D ALA* 1.3 59.1 + - - +
44D THR* 3.8 3.8 + - - -
50D LYS* 4.1 35.4 - - + +
51D ILE 3.3 12.6 - - - +
52D CYS* 3.9 3.8 - - - -
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Residues in contact with ALA 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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24D ILE* 3.9 36.8 - - + -
26D SER 3.6 5.2 - - - +
27D LEU* 4.1 10.3 - - + +
41D LEU 4.2 1.4 - - - -
42D ILE* 1.3 71.0 - - - +
44D THR* 1.3 61.6 + - - +
45D LEU 3.5 2.4 + - - +
49D ARG 3.6 0.2 - - - +
50D LYS* 3.5 4.1 - - - -
51D ILE* 2.9 49.6 + - + +
52D CYS* 4.9 0.2 - - - +
53D LEU* 4.8 4.9 - - + -
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS 4.1 18.6 - - - +
47A ASN 4.4 0.7 - - - +
48A GLY* 4.1 16.3 - - - +
24D ILE* 3.3 4.4 - - - -
25D THR* 2.8 29.1 + - - -
26D SER* 3.4 26.5 + - - -
42D ILE 3.8 2.7 + - - -
43D ALA* 1.3 70.2 - - - +
45D LEU* 1.3 74.3 + - - +
48D GLY* 4.2 5.8 - - - -
49D ARG 3.4 9.9 - - - +
50D LYS* 3.7 22.7 + - + +
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Residues in contact with LEU 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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47A ASN* 4.9 1.7 + - - +
19D VAL* 4.4 5.6 - - + -
20D ARG* 3.1 41.1 - - - +
23D HIS* 3.1 17.3 - - + +
24D ILE* 4.6 3.6 - - + -
25D THR* 4.5 3.9 + - - -
43D ALA 3.5 1.6 + - - +
44D THR* 1.3 91.9 - - - +
46D LYS* 1.3 66.9 + - - +
47D ASN* 3.3 28.9 - - - +
48D GLY 3.3 3.6 + - - -
49D ARG* 2.8 35.0 + - + +
51D ILE* 4.2 28.7 - - + -
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Residues in contact with LYS 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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47A ASN* 2.6 34.8 + - - +
31C LYS* 4.2 7.3 - - - +
22D ARG* 3.2 48.4 - - - +
23D HIS* 2.6 40.1 + - + +
24D ILE 5.0 3.0 + - - -
25D THR* 4.6 12.3 + - - +
45D LEU* 1.3 72.4 - - - +
47D ASN* 1.3 62.7 + - - +
48D GLY 3.1 4.3 + - - -
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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