Contacts of the strand formed by residues 74 - 87 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A CYS* 2.0 47.8 - - + -
9A GLN 4.0 2.5 - - - -
37A CYS* 3.6 31.4 - - - +
38A LYS 3.8 13.2 - - - -
39A GLY 3.4 21.6 + - - +
41A CYS* 3.8 4.5 - - - -
73A CYS* 1.3 77.7 - - - +
75A VAL* 1.3 63.3 + - - +
76A PRO* 4.8 0.2 - - - +
107A CYS* 4.6 4.0 - - - -
108A GLY 3.3 4.7 - - - -
73B CYS* 5.1 0.7 - - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A CYS* 3.5 6.3 - - - -
73A CYS* 4.1 4.9 - - + +
74A CYS* 1.3 78.1 - - - +
76A PRO* 1.3 78.9 - - + +
77A THR* 3.3 2.6 + - + -
107A CYS* 3.5 1.9 - - - -
108A GLY 2.9 34.9 + - - +
110A ARG* 3.7 33.0 - - + -
73B CYS* 3.9 15.0 - - + -
75B VAL* 3.2 36.1 - - + -
110B ARG* 4.2 13.7 - - + +
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A CYS* 3.4 22.4 - - + -
75A VAL* 1.3 93.3 - - + +
77A THR* 1.3 60.7 + - - +
78A LYS 4.8 0.2 - - - +
79A LEU* 4.1 20.7 - - + +
104A VAL* 4.1 24.5 - - + -
106A GLU 3.6 2.7 - - - +
52B THR* 6.0 0.2 - - - +
54B HIS* 4.3 11.7 - - + +
58B GLN* 5.5 0.9 - - - +
110B ARG* 3.3 40.8 - - + +
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 4.8 2.9 + - - -
75A VAL* 3.6 8.7 - - + +
76A PRO* 1.3 73.9 - - - +
78A LYS* 1.3 60.3 + - - +
79A LEU* 5.7 0.9 - - - -
106A GLU* 2.8 27.8 + - - +
107A CYS 3.3 8.7 + - - +
108A GLY* 3.4 30.3 - - - +
110A ARG* 3.4 37.5 + - + +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PRO 3.6 0.2 - - - -
77A THR* 1.3 81.3 + - - +
79A LEU* 1.3 73.1 + - - +
104A VAL* 4.0 0.5 - - - +
105A ALA* 2.8 38.4 + - + +
106A GLU* 3.4 41.8 + - + +
34E GLU* 3.7 24.9 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PRO* 4.1 20.0 - - + +
77A THR 5.7 0.4 - - - -
78A LYS* 1.3 87.7 - - - +
80A SER* 1.3 62.5 + - - +
81A PRO* 4.0 3.3 - - - +
100A GLU* 4.3 6.4 - - - +
101A GLY* 3.8 25.1 - - - +
103A SER 3.0 28.7 - - - +
104A VAL* 3.8 6.3 - - + -
105A ALA* 4.4 1.6 - - - -
52B THR* 3.8 37.2 - - + +
54B HIS* 4.3 12.1 - - + -
34E GLU* 5.2 1.9 - - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 1.3 73.4 - - - +
81A PRO* 1.3 72.5 - - - +
101A GLY 4.2 1.6 - - - -
102A MET 3.2 7.4 + - - -
103A SER* 3.0 42.5 + - - -
104A VAL 5.4 0.7 - - - -
105A ALA* 4.1 14.1 - - - +
34E GLU* 2.4 35.0 + - - -
37E LYS* 3.5 17.0 - - - +
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Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU 4.2 1.3 - - - +
80A SER* 1.3 93.8 - - - +
82A ILE* 1.3 66.8 + - - +
98A HIS* 4.1 20.4 - - + +
99A TYR 3.1 28.9 - - - +
100A GLU* 3.5 24.7 - - - +
101A GLY 4.0 2.9 - - - +
102A MET 4.5 0.4 - - - +
34E GLU* 4.1 9.4 - - - +
37E LYS* 5.7 1.6 - - - +
61E LEU* 3.7 23.4 - - + +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.7 2.5 - - + -
29A PRO* 5.5 1.6 - - + -
32A TYR* 3.7 43.1 - - + -
33A GLU 5.3 0.7 - - - +
81A PRO* 1.3 79.5 - - - +
83A SER* 1.3 62.7 + - - +
84A VAL* 3.9 20.2 - - + -
97A TYR 3.4 4.8 - - - +
99A TYR* 3.1 33.2 + - + +
102A MET* 3.8 34.9 - - + +
103A SER* 4.2 16.8 - - - -
61E LEU* 4.3 8.5 - - + +
62E ASP 5.4 8.1 - - - +
63E ASP* 6.4 1.8 - - + -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 3.8 5.0 - - - +
82A ILE* 1.3 74.5 - - - +
84A VAL* 1.3 70.8 + - - +
95A LEU* 4.4 0.9 - - - -
96A LYS 3.4 7.2 - - - -
97A TYR* 2.8 38.2 + - - -
60E TRP* 3.3 41.5 - - - +
61E LEU* 3.2 22.7 + - - +
63E ASP* 6.0 0.7 - - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 5.1 4.3 - - + -
25A TRP* 5.4 0.9 - - + -
26A ILE* 4.4 22.9 - - + -
28A ALA 3.4 12.1 - - - +
29A PRO* 4.3 4.7 - - + -
82A ILE* 3.9 18.8 - - + -
83A SER* 1.3 83.2 - - - +
85A LEU* 1.3 58.9 + - - +
86A TYR* 3.9 16.7 + - + -
94A THR 3.8 0.2 - - - +
95A LEU* 3.2 8.3 - - - +
96A LYS* 2.9 39.6 + - + +
99A TYR* 3.9 33.2 - - + -
60E TRP* 3.6 1.6 - - - -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.8 0.9 - - - -
27A ILE* 2.7 41.0 + - + +
28A ALA* 3.0 18.2 + - + +
84A VAL* 1.3 71.6 - - - +
86A TYR* 1.3 60.2 + - - +
93A PRO* 4.2 7.4 - - + -
94A THR* 3.1 30.7 - - - +
95A LEU* 4.3 9.4 - - + -
42E TYR* 4.8 6.5 - - + -
44E SER* 3.7 23.1 - - - +
56E LYS* 4.4 9.0 - - + -
60E TRP* 3.8 11.5 - - + -
81E VAL* 4.6 11.2 - - + -
83E PHE* 3.6 25.8 - - + -
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TRP* 2.9 45.1 - + + +
26A ILE* 4.3 5.4 - - + -
27A ILE* 3.9 6.7 - - - -
84A VAL* 4.0 16.6 - - + -
85A LEU* 1.3 75.0 - - - +
87A LYS* 1.3 75.8 + - - +
88A ASP* 4.4 3.8 - - - -
92A VAL 3.3 0.2 - - - +
93A PRO* 3.6 0.7 - - - +
94A THR* 2.9 60.8 + - - -
95A LEU 4.4 0.9 - - - -
96A LYS* 3.9 24.0 - - + -
78C ARG* 4.1 11.9 - - - -
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP 5.1 3.8 + - - -
24A SER 4.1 22.6 + - - +
25A TRP* 2.9 18.0 + - + +
27A ILE* 3.9 18.8 - - + +
86A TYR* 1.3 79.7 - - - +
88A ASP* 1.3 69.4 + - - +
91A GLY* 4.2 20.2 - - - +
92A VAL 3.8 3.6 - - - -
93A PRO* 5.3 1.8 - - + -
78C ARG* 3.0 21.5 + - - +
80E GLN* 3.5 33.3 + - - +
81E VAL* 5.8 2.5 - - - -
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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
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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