Contacts of the strand formed by residues 74 - 87 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G CYS* 2.0 46.4 - - - -
9G GLN 3.9 3.1 - - - -
37G CYS* 3.5 33.2 - - - +
38G LYS 3.8 12.8 - - - -
39G GLY 3.4 21.1 + - - +
41G CYS* 3.8 6.4 - - - -
73G CYS* 1.3 79.6 - - - +
75G VAL* 1.3 61.3 + - - +
107G CYS* 4.6 3.8 - - - -
108G GLY 3.2 6.5 - - - -
73H CYS* 5.1 0.5 - - - +
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G CYS* 3.6 4.9 - - - -
73G CYS* 4.1 5.6 - - + +
74G CYS* 1.3 79.9 - - - +
76G PRO* 1.3 81.9 - - + +
77G THR* 3.3 3.0 + - + +
107G CYS* 3.6 1.4 - - - -
108G GLY 2.9 30.8 + - - +
110G ARG* 3.7 31.9 - - + -
73H CYS* 3.8 16.8 - - + -
75H VAL* 3.3 33.7 - - + -
110H ARG* 4.4 9.9 - - + +
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Residues in contact with PRO 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G CYS* 3.5 22.4 - - + +
74G CYS 4.8 0.2 - - - +
75G VAL* 1.3 94.9 - - + +
77G THR* 1.3 59.0 + - - +
78G LYS 3.7 0.4 - - - -
79G LEU* 4.1 21.7 - - + +
104G VAL* 4.1 24.9 - - + -
106G GLU 3.7 2.7 - - - +
54H HIS* 4.4 11.7 - - + +
58H GLN* 5.2 1.6 - - - +
110H ARG* 3.4 39.7 - - + +
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Residues in contact with THR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G THR* 4.9 2.6 + - - -
75G VAL* 3.5 9.0 - - + +
76G PRO* 1.3 74.4 - - - +
78G LYS* 1.3 60.1 + - - +
79G LEU* 5.7 0.4 - - - -
106G GLU* 2.8 27.0 + - - +
107G CYS 3.3 8.2 + - - +
108G GLY* 3.4 34.5 - - - +
110G ARG* 3.5 32.2 + - + +
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Residues in contact with LYS 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G THR* 1.3 81.4 + - - +
79G LEU* 1.3 64.5 + - - +
104G VAL* 4.0 0.3 - - - +
105G ALA* 2.7 45.7 + - + +
106G GLU* 3.4 26.1 + - + +
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Residues in contact with LEU 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G PRO* 4.1 21.3 - - + +
77G THR 5.7 0.2 - - - -
78G LYS* 1.3 83.3 - - - +
80G SER* 1.3 61.9 + - - +
81G PRO* 4.0 2.9 - - - +
100G GLU* 4.2 7.8 - - - +
101G GLY* 3.8 26.8 - - - +
103G SER 3.0 29.2 - - - +
104G VAL* 3.7 7.0 - - + -
105G ALA* 4.4 1.6 - - - -
52H THR* 4.1 32.5 - - + +
54H HIS* 4.2 12.3 - - + -
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Residues in contact with SER 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G LEU* 1.3 72.9 - - - +
81G PRO* 1.3 74.8 - - - +
101G GLY 4.2 1.8 - - - -
102G MET 3.1 6.9 + - - -
103G SER* 3.0 42.7 + - - +
104G VAL 5.4 0.7 - - - -
105G ALA* 4.0 17.0 - - - +
34K GLU* 5.3 5.7 - - - +
37K LYS* 4.6 16.9 - - - +
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Residues in contact with PRO 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G LEU 4.1 1.1 - - - +
80G SER* 1.3 94.6 - - - +
82G ILE* 1.3 68.2 + - - +
98G HIS* 4.1 18.6 - - + +
99G TYR 3.1 29.6 - - - +
100G GLU* 3.4 29.6 - - - +
101G GLY 4.0 1.8 - - - +
102G MET 4.5 0.4 - - - +
61K LEU* 4.2 19.2 - - + +
62K ASP 5.8 0.2 - - - +
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G PHE* 4.7 1.8 - - + -
29G PRO* 5.4 1.1 - - + -
32G TYR* 3.7 43.1 - - + -
33G GLU 5.2 0.7 - - - +
81G PRO* 1.3 80.4 - - - +
83G SER* 1.3 63.5 + - - +
84G VAL* 3.8 20.9 - - + -
97G TYR 3.4 4.9 - - - +
99G TYR* 3.0 34.3 + - + +
102G MET* 3.8 33.8 - - + +
103G SER* 4.2 17.7 - - - -
61K LEU* 4.4 7.9 - - + +
62K ASP 5.1 10.3 - - - +
63K ASP* 6.3 3.1 - - + -
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Residues in contact with SER 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PRO* 3.8 4.7 - - - +
82G ILE* 1.3 74.3 - - - +
84G VAL* 1.3 70.6 + - - +
95G LEU* 4.4 1.3 - - - -
96G LYS 3.4 6.7 - - - -
97G TYR* 2.7 40.3 + - - -
60K TRP* 3.4 35.7 - - - -
61K LEU* 3.3 27.4 + - - +
63K ASP* 6.0 0.9 - - - +
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Residues in contact with VAL 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G PHE* 5.0 7.4 - - + -
25G TRP* 5.4 0.9 - - + -
26G ILE* 4.4 19.5 - - + -
28G ALA 3.3 12.6 - - - +
29G PRO* 4.3 4.7 - - + -
82G ILE* 3.8 25.6 - - + -
83G SER* 1.3 82.5 - - - +
85G LEU* 1.3 59.6 + - - +
86G TYR* 3.9 17.1 + - + -
94G THR 3.9 0.2 - - - +
95G LEU* 3.1 7.6 - - - +
96G LYS* 2.9 39.7 + - + +
99G TYR* 3.9 26.7 - - + -
60K TRP* 3.8 1.8 - - - -
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Residues in contact with LEU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ILE* 4.0 0.5 - - - -
27G ILE* 2.8 50.2 + - + +
28G ALA* 3.0 18.2 + - + +
84G VAL* 1.3 74.2 - - - +
86G TYR* 1.3 52.8 + - - +
93G PRO* 4.0 13.0 - - + -
94G THR* 3.1 33.0 - - - +
95G LEU* 4.3 6.5 - - + +
42K TYR* 4.5 8.1 - - + -
44K SER* 3.9 29.4 - - - +
56K LYS* 4.3 12.1 - - + -
60K TRP* 3.9 12.2 - - + -
81K VAL* 5.1 2.2 - - + -
83K PHE* 4.1 16.2 - - + -
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Residues in contact with TYR 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G TRP* 3.0 44.4 - + + +
26G ILE* 4.2 5.4 - - + -
27G ILE* 3.8 7.2 - - - -
84G VAL* 4.0 17.0 - - + -
85G LEU* 1.3 75.0 - - - +
87G LYS* 1.3 78.1 + - - +
88G ASP* 4.5 3.4 - - - -
92G VAL 3.3 0.3 - - - +
93G PRO* 3.6 0.2 - - - +
94G THR* 2.9 60.1 + - - -
95G LEU 4.3 0.9 - - - -
96G LYS* 3.9 21.9 - - + +
78J ARG* 4.0 12.6 - - - -
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Residues in contact with LYS 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ASP 5.1 4.2 + - - -
24G SER 4.1 21.9 + - - +
25G TRP* 2.9 18.7 + - + +
27G ILE* 3.9 21.0 - - + +
86G TYR* 1.3 80.1 - - - +
88G ASP* 1.3 67.8 + - - +
91G GLY* 4.1 20.6 - - - +
92G VAL 3.8 3.6 - - - -
93G PRO* 5.2 1.6 - - + -
78J ARG* 2.8 23.2 + - - +
80K GLN* 3.8 27.5 + - - +
81K VAL* 5.8 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