Contacts of the strand formed by residues 42 - 50 (chain B) in PDB entry 1RRP
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 CYS 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B GLU* 3.4 26.2 - - + +
41B PHE* 1.3 81.7 - - - +
43B ASN* 1.3 60.3 + - - +
64B ASN* 4.3 19.3 - - - -
65B VAL 3.4 7.0 - - - -
66B LYS* 3.9 21.8 - - + -
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.4 23.2 - - + -
42B CYS* 1.3 75.8 - - - +
44B ARG* 1.3 87.2 + - - +
64B ASN* 3.6 5.4 - - - -
65B VAL* 2.7 42.6 + - - +
131B PHE* 4.6 6.1 - - + -
136B GLU* 3.1 47.7 + - - +
139B LEU* 5.5 6.2 - - + +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN* 1.3 93.9 + - - +
45B ALA* 1.3 66.2 - - - +
62B ILE* 3.9 21.6 - - - +
63B GLY* 2.7 16.7 + - - +
64B ASN* 2.9 19.7 + - - +
83B GLU* 2.6 40.2 + - - +
131B PHE* 4.0 4.3 - - - -
132B LYS* 4.5 22.0 + - - +
136B GLU* 4.7 2.6 - - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN 3.8 0.8 + - - -
44B ARG* 1.3 79.2 - - - +
46B LYS* 1.3 62.3 + - - +
62B ILE* 3.3 7.4 - - - +
63B GLY 2.5 33.1 + - - -
65B VAL* 4.4 4.3 - - + -
80B MET* 3.0 7.6 - - + +
129B ILE* 4.0 14.4 - - + -
130B ARG 3.4 13.7 - - - +
131B PHE* 3.3 29.2 - - + +
132B LYS 6.0 0.4 - - - +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ASP* 2.7 33.9 + - - +
45B ALA* 1.3 75.8 - - - +
47B LEU* 1.3 59.3 + - - +
48B PHE* 3.3 31.2 - - + -
59B GLU* 3.7 26.7 + - + +
61B GLY 3.2 15.3 - - - +
62B ILE* 3.3 21.3 - - + -
129B ILE* 3.4 7.0 - - - +
130B ARG* 2.9 49.9 + - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS* 1.3 71.4 - - - +
48B PHE* 1.3 68.4 + - - +
59B GLU* 3.5 2.9 - - - +
60B ARG* 2.5 41.3 + - + -
61B GLY* 2.6 21.0 + - - +
80B MET* 3.6 25.5 - - - +
89B CYS* 2.8 33.0 - - - +
90B ALA* 4.0 8.7 - - + -
112B TRP* 4.0 15.5 - - + -
127B LEU* 4.4 11.9 - - + -
128B ALA 3.0 23.1 - - - +
129B ILE* 3.6 14.6 - - + -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.5 24.7 - - + -
210A PRO* 3.9 24.0 - - + -
211A ASP* 4.3 2.2 - - - -
46B LYS* 3.3 52.5 - - + -
47B LEU* 1.3 78.6 - - - +
49B ARG* 1.3 60.0 + - - +
57B TRP* 3.2 16.1 - - + -
58B LYS 3.2 17.5 - - - +
59B GLU* 4.0 14.8 - - + -
60B ARG* 4.2 1.6 - - - -
127B LEU* 3.2 10.6 - - - +
128B ALA* 2.6 51.9 + - + +
130B ARG* 3.6 26.7 - - + -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 3.8 32.9 + - - +
48B PHE* 1.3 72.7 - - - +
50B PHE* 1.3 86.2 + - - +
51B ASP* 6.1 0.2 - - - +
57B TRP* 3.1 4.7 - - - -
58B LYS* 2.9 43.8 + - - +
60B ARG* 3.9 37.4 - - + +
119B ASP* 5.2 2.0 + - - -
123B LYS* 5.7 3.6 - - - +
125B GLU* 3.6 49.9 + - + +
126B GLN 3.7 2.0 - - - -
127B LEU* 3.9 7.0 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 5.0 7.4 - - + -
204A ALA* 4.0 16.2 - - + -
207A THR* 3.6 25.1 - - - -
49B ARG* 1.3 98.1 + - - +
51B ASP* 1.3 72.7 + - - +
52B VAL* 3.0 44.7 - - + +
55B LYS* 3.1 39.7 - - + -
56B GLU 4.4 1.1 - - - -
57B TRP* 2.9 43.8 - + + -
58B LYS* 5.6 0.2 - - - -
126B GLN* 3.2 23.2 + - + +
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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