Contacts of the strand formed by residues 54 - 68 (chain C) in PDB entry 3RIE
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 GLN 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B TRP* 3.6 8.3 - - - -
56B PHE* 3.9 23.8 - - + -
57B SER 3.2 9.6 - - - +
58B LEU* 4.1 3.8 - - + -
82B TYR* 2.7 31.0 + - + -
46C GLU 4.1 1.2 - - - +
47C PHE* 4.6 3.6 - - - -
51C TRP* 3.4 41.4 - - + +
52C PRO 3.3 3.1 - - - +
53C GLY* 1.4 79.7 - - - +
55C ALA* 1.3 67.2 - - - +
56C PHE 6.1 0.2 - - - +
235C ILE* 3.7 12.8 - - - +
265C PRO* 4.0 12.9 - - - +
266C CYS* 3.7 29.4 - - - +
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TRP* 4.1 4.7 - - + -
55B ALA 3.9 0.3 - - - +
56B PHE* 3.5 8.6 - - - -
57B SER* 2.8 42.8 + - - -
45C SER* 5.0 2.2 - - - -
46C GLU 3.7 15.9 - - - +
47C PHE* 3.6 31.9 - - + -
51C TRP* 5.3 1.1 - - - -
54C GLN* 1.3 82.7 - - - +
56C PHE* 1.3 63.0 + - - +
57C SER* 4.2 2.0 + - - +
701C 1PG 5.6 0.9 - - - -
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Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 4.0 29.4 - - + -
55B ALA 3.4 16.2 - - - -
56B PHE* 4.6 12.1 - + + +
266B CYS* 5.5 4.5 - - - -
44C PHE* 5.2 1.2 - - - -
45C SER* 3.6 0.3 - - - -
46C GLU* 2.8 44.6 + - - +
54C GLN* 6.1 0.2 - - - +
55C ALA* 1.3 73.7 - - - +
57C SER* 1.3 57.2 + - - +
58C LEU* 3.6 39.5 - - + -
82C TYR* 4.5 7.4 - - - -
92C ILE* 4.0 17.3 - - + -
262C PRO* 4.4 13.0 - - + -
263C THR* 3.9 32.1 - - + -
264C TYR 6.3 0.7 - - - -
265C PRO* 5.8 6.3 - - + -
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 3.3 6.1 - - - +
55B ALA* 2.8 39.5 + - - +
57B SER* 5.0 1.6 + - - -
43C TRP* 3.7 19.7 - - - -
44C PHE* 2.9 12.1 - - - -
45C SER* 2.6 25.8 + - - -
55C ALA* 4.8 3.1 + - - +
56C PHE* 1.3 75.5 - - - +
58C LEU* 1.3 66.4 + - - +
92C ILE* 6.4 0.2 - - - -
701C 1PG 4.0 14.1 - - - -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY 3.4 10.5 - - - +
54B GLN* 4.1 1.3 - - + -
43C TRP* 3.4 4.4 - - - -
44C PHE* 2.8 35.3 + - + +
56C PHE* 3.6 30.5 - - + -
57C SER* 1.3 72.6 - - - +
59C LYS* 1.3 62.6 + - - +
60C ILE* 3.6 0.5 + - - +
77C PHE* 4.2 14.6 - - + -
79C SER* 4.4 9.0 - - - -
81C THR* 5.0 0.2 - - - +
82C TYR* 3.5 33.0 - - + -
85C VAL* 4.0 27.6 - - + -
92C ILE* 4.1 23.3 - - + -
95C THR* 4.4 9.6 - - + -
263C THR* 4.9 0.2 - - + -
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Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO* 6.3 0.6 - - - +
53B GLY* 2.8 25.2 + - - +
41C LYS* 4.0 25.8 - - + -
42C LYS 3.8 9.6 - - - +
43C TRP* 3.4 37.9 - - + +
58C LEU* 1.3 71.5 - - - +
60C ILE* 1.3 62.0 + - - +
79C SER* 3.1 8.1 - - - -
80C THR* 2.9 56.4 + - + +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.6 21.3 - - - +
42C LYS* 2.8 32.2 + - + +
43C TRP 3.6 8.1 - - - +
44C PHE* 3.5 36.8 - - + +
58C LEU 3.9 1.6 - - - +
59C LYS* 1.3 73.0 - - - +
61C LYS* 1.3 63.4 + - - +
62C LYS* 3.8 26.5 - - - +
63C ILE* 3.9 26.2 - - + +
75C LEU* 6.3 0.7 - - + -
77C PHE* 3.9 17.3 - - + -
78C GLU 3.8 5.2 - - - +
80C THR* 4.2 2.0 - - - -
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.9 21.8 - - - +
59C LYS 3.6 3.6 + - - -
60C ILE* 1.3 75.1 - - - +
62C LYS* 1.3 65.6 + - + +
78C GLU* 2.6 52.3 + - + +
79C SER 4.1 7.9 - - - +
80C THR* 4.0 20.7 + - + +
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Residues in contact with LYS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 3.8 8.1 - - - -
61C LYS* 1.3 85.8 - - + +
63C ILE* 1.3 67.6 + - - +
64C LEU* 3.6 25.0 - - + +
77C PHE* 3.5 1.2 - - - +
78C GLU* 2.7 56.9 + - + +
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 3.9 30.4 - - + +
62C LYS* 1.3 83.7 - - - +
64C LEU* 1.3 61.9 + - - +
65C TYR 3.9 10.5 - - - +
66C GLU* 3.8 25.4 - - + +
75C LEU* 4.1 15.5 - - + -
76C VAL 4.0 4.7 - - - +
77C PHE* 3.9 12.3 - - + -
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS* 3.6 37.9 + - + +
63C ILE* 1.3 76.0 - - - +
65C TYR* 1.3 63.6 + - - +
76C VAL* 2.9 21.9 + - + +
78C GLU* 4.1 11.4 - - + +
84C LYS* 3.7 37.7 - - + -
159C TYR* 3.3 36.1 + - + -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 3.8 3.7 - - - +
64C LEU* 1.3 79.8 - - - +
66C GLU* 1.3 72.6 + - - +
67C THR* 3.3 43.4 + - + +
74C VAL* 4.5 6.5 - - + -
75C LEU* 3.4 0.7 - - - +
76C VAL* 2.7 38.2 + - + +
151C THR* 4.9 2.6 - - - +
155C VAL* 3.5 32.6 - - + +
158C ILE* 5.9 5.6 - - + -
159C TYR* 3.7 29.6 - + + -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 3.8 18.6 - - + +
65C TYR* 1.3 86.3 - - - +
67C THR* 1.3 63.3 + - - +
74C VAL 3.2 9.2 - - - +
75C LEU* 3.5 23.9 - - + +
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Residues in contact with THR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TYR* 3.3 36.6 + - + +
66C GLU* 1.3 75.1 - - - +
68C LYS* 1.3 68.6 + - - +
69C SER* 4.9 0.4 - - - -
73C ASN* 3.7 1.7 - - - +
74C VAL* 2.8 39.8 + - + +
151C THR* 3.8 22.2 - - + -
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR* 1.3 79.8 + - - +
69C SER* 1.3 72.8 + - - +
72C GLN 3.6 6.3 - - - +
73C ASN* 3.3 26.4 + - - +
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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