Contacts of the strand formed by residues 54 - 68 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B PHE* 4.4 6.2 - - - +
51B TRP* 3.5 39.4 - - + +
52B PRO 4.4 3.3 - - - +
53B GLY* 1.4 77.9 + - - +
55B ALA* 1.3 65.6 + - - +
235B ILE* 4.8 3.5 - - - +
265B PRO* 4.1 13.1 - - - +
266B CYS* 3.4 37.4 - - - +
43C TRP* 3.6 7.7 - - - -
56C PHE* 4.0 21.9 - - + -
57C SER 3.3 11.2 - - - +
58C LEU* 4.1 5.2 - - + -
81C THR* 4.9 0.3 + - - -
82C TYR* 2.7 30.2 + - + -
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Residues in contact with ALA 55 (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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45B SER* 5.3 2.5 - - - -
46B GLU 3.4 17.9 - - - +
47B PHE* 4.2 14.6 - - + -
51B TRP* 5.5 1.6 - - - -
54B GLN* 1.3 78.7 - - - +
56B PHE* 1.3 62.4 + - - +
57B SER* 5.1 3.8 - - - +
43C TRP* 4.2 13.2 - - + -
55C ALA 3.9 0.3 - - - +
56C PHE* 3.4 10.5 - - - -
57C SER* 2.8 41.1 + - - +
701C 1PG 5.6 5.2 - - - -
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Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 4.1 0.7 - - - +
46B GLU* 2.8 46.6 + - - +
55B ALA* 1.3 75.9 - - - +
57B SER* 1.3 60.9 + - - +
58B LEU* 3.6 37.5 - - + -
82B TYR* 4.8 4.5 - + - -
92B ILE* 3.8 20.5 - - + +
262B PRO* 4.3 12.8 - - + -
263B THR* 3.7 32.1 - - + -
264B TYR 6.4 0.4 - - - -
265B PRO* 6.0 5.6 - - + -
54C GLN* 3.9 31.4 - - + -
55C ALA 3.5 15.0 - - - -
56C PHE* 4.6 11.0 - + + -
266C CYS* 5.8 3.1 - - - -
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Residues in contact with SER 57 (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 TRP* 3.7 19.1 - - - -
44B PHE 3.0 10.5 - - - -
45B SER* 2.6 26.2 + - - -
55B ALA* 5.1 1.2 - - - +
56B PHE* 1.3 78.1 + - - +
58B LEU* 1.3 66.7 + - - +
54C GLN* 3.2 5.7 - - - +
55C ALA* 2.8 42.2 + - - -
57C SER* 5.0 2.1 + - - -
701C 1PG 4.0 15.8 - - - -
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Residues in contact with LEU 58 (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 TRP* 3.5 3.3 - - - -
44B PHE* 2.7 40.2 + - + +
56B PHE* 3.6 34.1 - - + -
57B SER* 1.3 74.8 - - - +
59B LYS* 1.3 60.2 + - - +
60B ILE* 3.5 0.5 + - - +
77B PHE* 4.3 17.7 - - + -
79B SER* 4.4 5.8 - - - -
82B TYR* 3.7 29.4 - - + -
85B VAL* 4.0 26.2 - - + -
92B ILE* 4.3 13.9 - - + -
95B THR* 4.3 13.7 - - + -
263B THR* 4.5 1.3 - - + -
53C GLY 3.3 13.7 - - - +
54C GLN* 4.1 0.7 - - + -
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Residues in contact with LYS 59 (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 LYS* 3.7 39.1 - - + +
42B LYS 3.8 4.9 - - - +
43B TRP* 3.4 40.7 - - + +
58B LEU* 1.3 71.8 - - - +
60B ILE* 1.3 61.8 + - - +
79B SER* 3.3 6.9 - - - -
80B THR* 3.0 48.9 + - + +
53C GLY* 3.0 18.7 + - - +
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Residues in contact with ILE 60 (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 LYS* 3.2 25.3 - - - +
42B LYS* 2.7 43.5 + - + +
43B TRP 3.6 7.4 - - - -
44B PHE* 3.5 33.2 - - + +
59B LYS* 1.3 71.2 - - - +
61B LYS* 1.3 62.2 + - - +
62B LYS* 3.5 28.7 - - - +
63B ILE* 4.1 24.0 - - + +
75B LEU* 6.3 0.7 - - + -
77B PHE* 3.8 22.4 - - + -
78B GLU 3.9 4.7 - - - +
80B THR* 4.1 2.7 - - - -
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Residues in contact with LYS 61 (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 LYS* 4.0 20.1 - - - +
59B LYS 3.7 3.2 + - - -
60B ILE* 1.3 74.0 - - - +
62B LYS* 1.3 74.4 + - - +
78B GLU* 2.7 51.0 + - + +
79B SER 4.1 4.5 - - - +
80B THR* 3.8 16.2 - - + +
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Residues in contact with LYS 62 (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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62A LYS* 6.3 2.5 - - - -
60B ILE* 3.5 9.8 - - - +
61B LYS* 1.3 93.6 - - - +
63B ILE* 1.3 61.4 + - - +
64B LEU* 3.6 27.1 - - + +
77B PHE* 3.5 1.0 - - - +
78B GLU* 2.7 53.6 + - - +
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Residues in contact with ILE 63 (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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42B LYS* 6.0 0.7 - - - +
60B ILE* 4.2 25.6 - - + -
62B LYS* 1.3 75.3 - - - +
64B LEU* 1.3 67.7 + - - +
65B TYR 4.0 13.2 - - - +
66B GLU* 3.9 22.9 - - + +
75B LEU* 4.1 22.4 - - + -
76B VAL 4.1 4.3 - - - +
77B PHE* 3.9 13.2 - - + -
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Residues in contact with LEU 64 (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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64A LEU 6.1 1.1 - - - +
158A ILE* 5.8 0.3 - - - +
159A TYR* 4.3 7.6 + - - -
62B LYS* 3.6 40.8 - - + +
63B ILE* 1.3 76.6 - - - +
65B TYR* 1.3 64.5 + - - +
76B VAL* 2.7 20.0 + - + +
78B GLU* 4.2 10.8 - - + +
84B LYS* 3.7 37.0 - - + -
159B TYR* 3.8 35.2 + - + -
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Residues in contact with TYR 65 (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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158A ILE* 4.0 33.6 - - + +
161A LYS* 5.8 4.9 - - - -
63B ILE* 3.7 3.6 - - - +
64B LEU* 1.3 81.0 - - - +
66B GLU* 1.3 66.4 + - - +
67B THR* 2.6 41.6 - - + +
74B VAL* 3.9 12.1 - - + -
75B LEU* 3.5 2.6 - - - +
76B VAL* 2.7 49.4 + - + +
151B THR* 3.7 13.2 - - + +
155B VAL* 3.4 25.0 - - + +
159B TYR* 3.7 31.6 - + + -
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Residues in contact with GLU 66 (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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161A LYS* 5.5 3.3 + - - -
63B ILE* 3.9 20.3 - - + +
65B TYR* 1.3 80.4 - - - +
67B THR* 1.3 66.7 + - - +
74B VAL 3.3 11.2 - - - +
75B LEU* 4.2 21.6 - - + +
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Residues in contact with THR 67 (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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161A LYS* 4.9 11.2 + - - -
65B TYR* 2.6 42.6 - - + +
66B GLU* 1.3 78.0 - - - +
68B LYS* 1.3 74.5 + - - +
69B SER* 4.7 0.4 - - - +
73B ASN* 3.8 1.8 - - - +
74B VAL* 2.9 35.0 + - + +
151B THR* 4.6 7.0 - - + -
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Residues in contact with LYS 68 (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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67B THR* 1.3 83.4 + - - +
69B SER* 1.3 71.5 + - - +
71B TYR 5.7 0.6 - - - -
72B GLN* 3.8 9.8 - - - +
73B ASN* 2.9 40.3 + - - +
89B ASP* 5.4 0.4 + - - -
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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