Contacts of the strand formed by residues 77 - 92 (chain F) in PDB entry 3EO1
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 77 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C CYS 6.0 1.1 - - - -
77C CYS* 2.0 48.9 - - + -
78C CYS* 4.1 11.6 + - - +
79C VAL* 3.7 9.2 - - + -
48F CYS* 3.5 5.6 - - - -
75F SER 3.6 4.0 + - - -
76F PRO* 1.3 73.9 - - - +
78F CYS* 1.3 58.7 + - - +
79F VAL* 3.8 0.6 + - - -
110F LYS 3.6 0.2 - - - +
111F CYS* 2.9 7.4 - - - -
112F SER 2.6 42.7 + - - +
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Residues in contact with CYS 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C CYS* 3.9 13.9 + - - +
112C SER 5.2 0.3 - - - +
15F CYS* 2.0 52.3 - - + -
16F CYS 3.7 3.1 - - - -
44F CYS* 3.4 36.9 - - + +
45F SER* 3.7 14.6 - - - +
46F GLY 3.7 14.8 - - - +
48F CYS* 3.8 0.8 - - - -
77F CYS* 1.3 72.9 - - - +
79F VAL* 1.3 67.8 + - - +
80F PRO* 4.8 0.3 - - - +
109F CYS* 4.0 1.1 - - - -
110F LYS 3.6 3.4 - - - -
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C CYS* 3.7 14.8 - - + -
79C VAL* 3.5 32.5 - - + -
112C SER* 3.8 19.7 - - - +
78F CYS* 1.3 81.3 - - - +
80F PRO* 1.3 79.7 - - + +
109F CYS* 2.7 16.8 - - - -
110F LYS* 3.0 40.2 + - - +
112F SER* 3.8 18.6 - - - +
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Residues in contact with PRO 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 5.6 0.9 - - - +
58C HIS* 4.7 12.8 - - + +
59C SER* 5.0 2.5 - - - +
112C SER* 3.5 32.3 + - - +
44F CYS* 3.6 15.7 - - + +
79F VAL* 1.3 92.9 - - + +
81F GLN* 1.3 59.4 + - - +
83F LEU* 3.9 25.0 - - + +
106F VAL* 3.9 22.7 - - + -
108F SER 3.8 2.0 - - - +
109F CYS* 3.2 8.7 - - - -
110F LYS* 3.6 14.2 + - - -
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Residues in contact with GLN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ASP* 5.7 0.6 + - - -
80F PRO* 1.3 74.5 - - - +
82F ASP* 1.3 79.2 + - - +
83F LEU* 4.2 6.5 - - - +
108F SER* 2.8 27.2 + - - +
109F CYS* 3.8 10.3 - - - +
110F LYS* 3.6 38.3 + - + +
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Residues in contact with ASP 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F GLN* 1.3 96.6 + - - +
83F LEU* 1.3 61.3 + - - +
84F GLU* 6.1 0.2 - - - -
106F VAL* 3.8 2.4 - - - +
107F LYS* 2.8 34.5 + - + -
108F SER* 2.7 28.6 + - - +
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 6.1 0.4 - - - +
56C THR* 4.0 15.7 - - + +
58C HIS* 3.6 38.4 - - + +
80F PRO* 3.9 28.7 - - + +
81F GLN 4.3 6.5 - - - +
82F ASP* 1.3 83.0 + - - +
84F GLU* 1.3 64.2 + - - +
85F PRO* 4.5 1.0 - - - +
103F ASN* 3.5 39.5 + - + +
105F VAL 3.0 11.0 - - - +
106F VAL* 4.5 0.9 - - - -
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Residues in contact with GLU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ASP 4.3 0.4 + - - -
83F LEU* 1.3 73.8 - - - +
85F PRO* 1.3 74.9 - - + +
103F ASN 4.6 1.8 - - - -
104F MET 3.0 7.8 + - - -
105F VAL* 2.7 42.2 + - + +
107F LYS* 2.7 45.5 + - + +
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Residues in contact with PRO 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LEU 4.5 1.8 - - - +
84F GLU* 1.3 102.0 - - + +
86F LEU* 1.3 58.9 + - - +
87F THR 4.2 0.8 + - - -
100F GLN* 3.5 36.6 - - + +
101F LEU 3.1 20.4 - - - +
102F SER* 4.1 5.6 - - - -
103F ASN 4.4 4.0 - - - +
104F MET* 4.5 0.7 - - - +
105F VAL* 5.0 3.6 - - - +
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 3.7 22.4 - - + -
36F PRO* 4.6 6.1 - - + -
39F TYR* 3.4 49.4 - - + -
40F TYR 5.4 0.7 - - - +
85F PRO* 1.3 73.9 - - - +
87F THR* 1.3 70.8 + - - +
88F ILE* 3.9 12.6 - - + +
100F GLN* 4.5 0.9 - - - -
101F LEU* 2.9 32.0 + - - +
104F MET* 3.8 24.1 - - + +
105F VAL* 4.8 6.7 - - + -
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Residues in contact with THR 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F PRO* 4.0 7.6 - - - +
85F PRO 4.2 1.2 + - - -
86F LEU* 1.3 83.1 - - - +
88F ILE* 1.3 71.7 + - - +
98F VAL* 3.6 26.7 - - + -
99F GLU 3.4 15.3 - - - +
100F GLN* 3.9 19.6 + - + +
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 4.3 8.1 - - + -
32F TRP* 3.4 39.5 - - + -
33F VAL* 3.9 10.8 - - + -
35F GLU 3.4 8.3 - - - +
36F PRO* 4.1 7.9 - - + -
86F LEU* 3.9 24.2 - - + +
87F THR* 1.3 82.6 - - - +
89F LEU* 1.3 61.6 + - - +
90F TYR* 3.8 15.7 - - + -
97F LYS 3.6 0.3 - - - +
98F VAL* 3.3 27.3 - - - +
99F GLU 2.9 15.6 + - - +
101F LEU* 3.6 31.6 - - + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F VAL* 3.7 1.5 - - - +
34F HIS* 2.5 66.8 + - + +
35F GLU* 2.6 31.9 + - + +
88F ILE* 1.3 75.1 - - - +
90F TYR* 1.3 54.7 + - - +
91F TYR* 4.5 8.1 - - + +
96F PRO* 4.5 10.3 - - + -
97F LYS 3.4 16.2 - - - +
98F VAL* 3.4 29.8 - - + -
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ILE* 4.8 1.1 - - + -
57E ILE* 3.9 26.4 - - + +
59E ASN* 5.9 2.7 - - + +
103E VAL* 4.1 23.1 - - + -
32F TRP* 3.5 31.2 - + + +
33F VAL* 4.3 1.3 - - - -
34F HIS* 4.1 4.9 - - - +
88F ILE* 3.8 20.9 - - + -
89F LEU* 1.3 75.4 - - - +
91F TYR* 1.3 64.3 + - - +
92F VAL* 3.9 24.0 - - + -
97F LYS* 3.0 59.1 + - + +
99F GLU* 3.0 36.4 + - + -
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU* 5.0 12.1 - - + +
103E VAL* 4.1 19.8 + - - +
104E LEU 5.0 0.3 + - - -
32F TRP 4.7 3.6 + - - +
34F HIS* 3.1 44.3 + + + +
89F LEU* 4.5 8.1 - - + +
90F TYR* 1.3 80.0 - - - +
92F VAL* 1.3 60.7 + - - +
93F GLY 3.7 12.0 + - - +
94F ARG* 3.2 22.0 - - - -
95F THR 3.1 16.4 - - - -
96F PRO* 3.2 38.5 - - + +
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Residues in contact with VAL 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D SER* 4.0 13.8 + - - -
59E ASN* 4.6 12.8 - - + +
103E VAL* 4.5 9.4 - - + -
104E LEU* 3.5 33.9 - - + -
90F TYR* 3.9 23.8 - - + -
91F TYR* 1.3 73.2 - - - +
93F GLY* 1.3 60.7 + - - +
94F ARG 2.7 11.3 + - - -
95F THR* 2.9 33.7 + - + +
97F LYS* 3.9 24.5 - - + +
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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
------------------------------------------------------------
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