Contacts of the strand formed by residues 74 - 87 (chain B) in PDB entry 4FAO
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 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A CYS* 5.1 0.9 - - - +
8B CYS* 2.0 45.8 - - + -
9B GLN 3.9 3.6 - - - -
37B CYS* 3.5 32.4 - - - +
38B LYS 3.7 13.5 - - - -
39B GLY 3.4 22.2 + - - +
41B CYS* 3.8 5.5 - - - -
72B ALA 4.1 0.2 + - - -
73B CYS* 1.3 78.8 - - - +
75B VAL* 1.3 63.2 + - - +
107B CYS* 4.6 4.3 - - - -
108B GLY 3.2 5.8 - - - -
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Residues in contact with VAL 75 (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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73A CYS* 3.7 18.4 - - + -
75A VAL* 3.2 35.0 - - + -
110A ARG* 4.3 9.9 - - + +
37B CYS* 3.5 6.0 - - - -
73B CYS 4.1 4.3 - - - +
74B CYS* 1.3 79.4 - - - +
76B PRO* 1.3 80.8 - - + +
77B THR* 3.3 2.6 + - + -
107B CYS* 3.6 1.2 - - - -
108B GLY 2.9 29.7 + - - +
110B ARG* 3.7 32.3 - - + -
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Residues in contact with PRO 76 (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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54A HIS* 4.4 10.8 - - + +
58A GLN* 5.3 1.8 - - - +
110A ARG* 3.4 41.0 - - + +
37B CYS* 3.4 21.5 - - + +
74B CYS 4.8 0.2 - - - +
75B VAL* 1.3 95.2 - - + +
77B THR* 1.3 60.7 + - - +
78B LYS 5.2 0.2 - - - -
79B LEU* 4.1 21.6 - - + +
104B VAL* 4.1 24.9 - - + -
106B GLU 3.7 4.0 - - - +
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Residues in contact with THR 77 (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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50B THR* 4.9 1.9 + - - -
75B VAL* 3.5 8.3 - - + +
76B PRO* 1.3 74.9 - - - +
78B LYS* 1.3 60.1 + - - +
79B LEU* 5.7 0.9 - - - -
106B GLU* 2.8 27.8 + - - +
107B CYS 3.3 8.4 + - - +
108B GLY* 3.4 34.5 - - - +
110B ARG* 3.4 33.7 + - + +
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Residues in contact with LYS 78 (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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76B PRO 3.7 0.2 - - - -
77B THR* 1.3 81.7 + - - +
79B LEU* 1.3 68.5 + - - +
80B SER* 6.2 0.2 - - - -
104B VAL* 4.0 0.5 - - - +
105B ALA* 2.7 47.3 + - + +
106B GLU* 3.4 41.0 + - + +
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Residues in contact with LEU 79 (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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52A THR* 3.9 37.0 - - + +
54A HIS* 4.2 13.5 - - + -
110A ARG* 6.1 0.4 - - - -
76B PRO* 4.1 20.0 - - + +
77B THR 5.7 0.4 - - - -
78B LYS* 1.3 87.3 - - - +
80B SER* 1.3 61.5 + - - +
81B PRO* 4.2 2.6 - - - +
100B GLU* 4.3 7.3 - - - +
101B GLY* 3.8 24.0 - - - +
103B SER 3.0 28.5 - - - +
104B VAL* 3.8 6.5 - - + -
105B ALA* 4.4 1.6 - - - -
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Residues in contact with SER 80 (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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79B LEU* 1.3 73.0 - - - +
81B PRO* 1.3 69.7 - - - +
101B GLY 4.1 1.6 - - - -
102B MET 3.1 6.8 + - - -
103B SER* 3.1 37.5 + - - -
104B VAL 5.4 0.2 - - - -
105B ALA* 4.0 15.6 - - - +
34F GLU* 5.3 2.8 - - - +
37F LYS* 2.8 46.9 - - - +
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Residues in contact with PRO 81 (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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79B LEU 4.2 1.1 - - - +
80B SER* 1.3 94.0 - - - +
82B ILE* 1.3 67.5 + - - +
98B HIS* 4.1 16.2 - - + +
99B TYR 3.1 29.2 - - - +
100B GLU* 3.4 30.5 - - - +
101B GLY 4.0 2.0 - - - +
102B MET 4.5 0.4 - - - +
37F LYS* 4.5 5.8 + - + +
61F LEU* 4.1 19.4 - - + +
62F ASP 5.8 0.2 - - - +
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Residues in contact with ILE 82 (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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17B PHE* 4.7 2.0 - - + -
29B PRO* 5.4 1.3 - - + -
32B TYR* 3.6 47.6 - - + -
33B GLU 5.2 0.7 - - - +
81B PRO* 1.3 78.7 - - - +
83B SER* 1.3 62.6 + - - +
84B VAL* 3.8 21.1 - - + -
97B TYR 3.4 4.7 - - - +
99B TYR* 3.1 33.6 + - + +
102B MET* 3.8 28.9 - - + +
103B SER* 4.2 17.9 - - - -
37F LYS* 5.7 2.0 - - - +
61F LEU* 4.4 7.9 - - - +
62F ASP 5.1 9.9 - - - +
63F ASP* 6.3 2.2 - - + -
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Residues in contact with SER 83 (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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29B PRO* 3.8 5.0 - - - +
82B ILE* 1.3 75.0 - - - +
84B VAL* 1.3 70.1 + - - +
95B LEU* 4.4 1.1 - - - -
96B LYS 3.4 7.4 - - - -
97B TYR* 2.8 39.2 + - - -
60F TRP* 3.3 37.0 - - - -
61F LEU* 3.2 27.7 + - - +
63F ASP* 6.0 0.9 - - - +
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Residues in contact with VAL 84 (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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17B PHE* 5.0 7.0 - - + -
25B TRP* 5.3 1.3 - - + -
26B ILE* 4.2 23.3 - - + -
28B ALA 3.3 12.6 - - - +
29B PRO* 4.4 4.3 - - + -
82B ILE* 3.8 26.9 - - + -
83B SER* 1.3 82.8 - - - +
85B LEU* 1.3 59.7 + - - +
86B TYR* 4.0 14.0 + - + -
94B THR 3.8 0.3 - - - +
95B LEU* 3.2 8.2 - - - +
96B LYS* 2.9 39.9 + - + +
99B TYR* 3.9 26.5 - - + -
60F TRP* 3.7 1.1 - - - -
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Residues in contact with LEU 85 (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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26B ILE* 3.8 0.7 - - - -
27B ILE* 2.7 52.3 + - + +
28B ALA* 3.0 18.5 + - + +
84B VAL* 1.3 71.5 - - - +
86B TYR* 1.3 54.0 + - - +
93B PRO* 4.0 11.0 - - + -
94B THR* 3.1 32.8 - - - +
95B LEU* 4.3 6.3 - - + +
42F TYR* 4.6 6.7 - - + -
44F SER* 3.9 23.3 - - - +
56F LYS* 4.3 12.3 - - + -
60F TRP* 3.8 12.2 - - + -
81F VAL* 4.9 1.3 - - + -
83F PHE* 3.8 24.9 - - + -
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Residues in contact with TYR 86 (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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25B TRP* 3.0 43.1 - + + +
26B ILE* 4.2 7.0 - - + -
27B ILE* 3.8 7.0 - - - -
84B VAL* 4.0 15.7 - - + -
85B LEU* 1.3 74.6 - - - +
87B LYS* 1.3 76.7 + - - +
88B ASP* 4.4 3.8 - - - -
92B VAL 3.3 0.2 - - - +
93B PRO* 3.6 0.2 - - - +
94B THR* 2.9 65.1 + - - -
95B LEU 4.3 0.9 - - - -
96B LYS* 3.9 22.2 - - + +
78D ARG* 4.0 13.2 - - - -
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Residues in contact with LYS 87 (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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23B ASP 5.1 4.4 + - - -
24B SER* 4.1 21.0 + - - +
25B TRP* 2.9 19.2 + - + +
27B ILE* 3.9 20.1 - - + +
86B TYR* 1.3 77.5 - - - +
88B ASP* 1.3 69.5 + - - +
91B GLY* 4.2 20.6 - - - +
92B VAL 3.8 4.3 - - - -
93B PRO* 5.3 1.6 - - + -
78D ARG* 2.9 22.3 + - - +
80F GLN* 3.6 30.9 + - - +
81F VAL* 5.7 2.9 - - - -
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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