Contacts of the strand formed by residues 33 - 39 (chain H) in PDB entry 3RWR
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 GLY 33 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.3 5.0 - - - +
30H THR* 2.8 31.7 + - - +
32H GLN* 1.3 77.9 - - - +
34H TYR* 1.3 60.2 + - - -
49H VAL 3.1 14.4 - - - -
50H ASP* 4.1 2.9 - - - -
54H VAL* 4.5 0.4 - - - -
73H LEU* 3.2 28.8 - - - +
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Residues in contact with TYR 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.5 5.6 - - - +
27H VAL* 4.7 2.2 - - + -
28H PHE 3.2 15.3 - - - +
29H ILE* 3.6 23.6 - - + -
33H GLY* 1.3 73.0 - - - +
35H ALA* 1.3 65.2 + - - +
36H LEU* 3.9 11.9 - - + -
47H GLU* 3.1 32.1 + - - -
48H GLN* 3.5 2.3 + - - -
49H VAL* 3.0 48.9 + - + +
57H ARG* 3.5 6.9 + - - -
73H LEU* 3.4 26.0 - - + -
76H LEU* 4.5 4.5 - - + -
119H TRP* 3.0 38.7 - + - -
121H PHE* 3.3 26.9 - + - -
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.2 16.8 - - + -
5H GLU* 3.1 19.5 - - - +
8H LEU* 3.1 26.3 - - + +
28H PHE 3.1 14.1 + - - -
34H TYR* 1.3 73.0 - - - +
36H LEU* 1.3 60.8 + - - +
46H HIS* 4.0 4.7 - - + -
47H GLU 3.6 7.6 - - - -
48H GLN* 3.1 24.9 - - - +
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Residues in contact with LEU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ALA* 4.1 5.2 - - + -
26H LYS 3.2 21.5 - - - +
27H VAL* 3.5 26.9 - - + -
34H TYR* 3.9 5.4 - - + -
35H ALA* 1.3 73.2 - - - +
37H LEU* 1.3 62.6 + - - +
38H VAL* 3.4 29.2 - - + -
46H HIS* 3.0 19.6 + - - -
47H GLU 3.2 17.3 + - - +
80H LEU* 6.4 0.2 - - + -
106H LEU* 4.1 9.9 - - + -
121H PHE* 3.5 44.4 - - + -
123H CYS* 3.9 10.6 - - - -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 3.8 19.7 - - + +
13H TRP* 3.5 24.4 - - + -
25H ALA* 3.1 1.7 - - - +
26H LYS* 2.8 47.3 + - + +
36H LEU* 1.3 72.7 - - - +
38H VAL* 1.3 61.7 + - - +
44H VAL* 3.6 15.7 - - + -
45H TRP 3.0 23.3 - - - +
46H HIS* 3.9 2.5 - - + +
130H LEU* 3.5 31.9 - - + -
134H HIS* 3.3 37.0 - - + +
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TRP* 4.8 0.9 - - - -
23H LEU* 3.4 41.5 - - + -
24H LEU 4.3 0.2 - - - -
25H ALA* 3.3 27.4 - - + +
36H LEU* 3.4 30.5 - - + -
37H LEU* 1.3 76.4 - - - +
39H SER* 1.3 68.7 + - - +
44H VAL* 3.6 1.9 - - - +
45H TRP* 2.6 51.2 + - + +
104H LEU* 5.6 2.9 - - + -
106H LEU* 4.4 11.0 - - + -
123H CYS* 4.6 6.5 - - + -
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TRP* 4.2 14.8 - - - -
23H LEU* 3.1 19.8 - - - +
24H LEU* 3.2 22.9 + - - +
38H VAL* 1.3 80.9 - - - +
40H ASP* 1.3 62.7 + - - +
41H LEU* 3.2 15.4 + - - +
43H GLN 3.5 15.8 + - - -
44H VAL* 3.6 24.7 + - - +
45H TRP* 4.3 3.4 - - - -
135H LEU* 4.9 3.6 - - - +
636I ILE* 5.6 1.9 - - - +
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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