Contacts of the strand formed by residues 38 - 44 (chain D) in PDB entry 2RHB
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 ILE 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D LYS* 4.1 1.1 - - - -
35D VAL* 2.8 51.3 + - + +
36D ASP* 3.1 8.5 + - + +
37D GLY* 1.3 80.3 - - - +
39D ASP* 1.3 65.3 + - - +
40D VAL* 3.7 1.9 + - + +
73F ASN* 5.9 3.1 - - - +
87F ASP* 5.5 0.2 - - - +
90F ARG* 3.7 35.9 - - - +
93F PRO 4.6 1.3 - - - +
94F ALA 3.4 30.3 - - - +
95F HIS* 4.2 1.6 - - - -
96F VAL* 3.9 24.2 - - + +
271F MET* 4.3 19.7 - - - -
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Residues in contact with ASP 39 (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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104B MET* 4.2 7.3 - - - +
25D SER* 4.4 7.2 + - - -
32D TYR* 4.0 26.2 - - + +
33D THR 3.4 4.9 - - - +
34D LYS* 3.3 34.2 + - - +
38D ILE* 1.3 73.0 - - - +
40D VAL* 1.3 57.4 + - - +
41D GLU 4.2 0.8 + - - -
48F THR* 2.7 33.6 + - + +
90F ARG* 2.5 31.1 + - - +
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Residues in contact with VAL 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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32D TYR* 3.9 2.7 - - - -
33D THR* 2.7 53.2 + - + +
35D VAL* 3.9 17.3 - - + -
38D ILE* 4.7 2.7 - - + +
39D ASP* 1.3 73.7 - - - +
41D GLU* 1.3 65.6 + - - +
42D ILE* 3.3 4.4 + - + +
90F ARG* 4.4 13.0 - - + +
269F ILE* 3.8 17.3 - - + -
270F PRO* 3.9 29.4 - - + +
271F MET* 3.9 25.4 - - + +
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Residues in contact with GLU 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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30D ALA* 3.4 18.4 - - - +
31D VAL 3.6 6.5 - - - +
32D TYR* 3.4 39.3 + - + -
39D ASP 4.3 0.2 + - - -
40D VAL* 1.3 71.4 - - - +
42D ILE* 1.3 60.2 + - - +
43D PHE 3.8 14.8 - - - +
44D GLU* 3.0 30.0 - - - +
46F LYS* 4.5 13.2 + - - +
90F ARG* 5.8 0.6 - - - +
270F PRO* 3.1 28.8 - - + +
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Residues in contact with ILE 42 (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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6D ALA* 4.3 9.6 - - + -
9D VAL* 4.2 10.3 - - + +
10D VAL* 4.1 22.0 - - + -
31D VAL* 2.8 27.2 + - + +
33D THR* 3.8 20.6 - - + +
40D VAL 3.6 14.8 - - - +
41D GLU* 1.3 76.3 - - - +
43D PHE* 1.3 61.0 + - - +
55D PHE* 3.7 28.5 - - + -
58D TRP* 3.9 19.8 - - - -
268F PHE* 3.6 25.7 - - - +
269F ILE* 4.6 5.2 - - + -
270F PRO* 4.4 5.8 - - + -
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Residues in contact with PHE 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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30D ALA* 3.3 7.3 - - - +
31D VAL* 2.9 38.5 + - + +
41D GLU* 3.7 5.8 - - - +
42D ILE* 1.3 82.0 - - - +
44D GLU* 1.3 74.0 + - - +
45D ASN* 3.8 21.8 - - + -
46D LYS 5.1 1.1 - - - -
47D THR* 5.4 0.4 - - + -
51D VAL* 3.9 8.7 - - + -
54D ALA* 3.9 13.7 - - + -
55D PHE* 3.4 55.2 - + + -
58D TRP* 3.6 44.0 - + + -
86D TRP* 4.6 11.0 - + - -
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Residues in contact with GLU 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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28D ASN 5.8 1.1 - - - +
29D ASN 4.1 3.6 - - - +
30D ALA* 4.4 4.0 - - + -
41D GLU* 3.0 28.0 - - - +
43D PHE* 1.3 90.1 - - - +
45D ASN* 1.3 67.1 + - - +
46D LYS* 3.2 44.2 + - + +
91D GLU* 5.0 2.0 - - - +
46F LYS* 3.8 17.5 + - - -
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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