Contacts of the strand formed by residues 69 - 76 (chain A) in PDB entry 2FV7
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 THR 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 4.0 3.9 - - - +
18A VAL* 3.2 20.2 - - + -
59A CYS* 3.7 14.1 - - - +
62A ALA* 4.1 5.8 - - + -
63A ALA* 3.8 17.1 - - - +
67A ALA* 3.3 27.6 + - + +
68A MET* 1.3 78.3 - - - +
70A SER* 1.3 60.3 + - - +
92A ASP 4.4 3.3 + - - +
93A ILE* 3.3 30.3 - - - +
94A SER* 3.0 28.3 + - - -
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Residues in contact with SER 70 (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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16A ALA* 3.8 18.4 - - - -
18A VAL 3.1 6.0 + - - +
19A VAL* 3.5 7.0 - - - +
20A VAL* 2.9 27.7 + - - +
59A CYS* 4.2 4.4 - - - -
69A THR* 1.3 76.3 - - - +
71A MET* 1.3 65.0 + - - +
72A VAL* 3.9 2.5 + - - +
93A ILE* 4.3 0.2 - - - -
94A SER* 3.7 20.7 + - - -
97A PHE* 3.9 23.9 + - - +
142A VAL* 4.1 10.7 - - - +
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Residues in contact with MET 71 (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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20A VAL* 3.6 17.9 - - + +
22A GLY 3.6 28.5 - - - +
23A SER 3.8 4.0 - - - +
24A CYS* 4.2 2.2 - - - -
55A GLY 3.7 10.1 - - - +
56A ALA* 3.6 23.3 - - - +
59A CYS* 3.7 26.2 - - - -
70A SER* 1.3 73.9 + - - +
72A VAL* 1.3 60.0 + - - +
73A CYS* 3.9 19.7 - - + -
88A LEU* 4.0 19.7 - - + -
93A ILE* 3.9 17.2 - - + +
94A SER 3.3 8.9 + - - +
97A PHE* 3.3 15.4 - - - +
98A THR* 3.3 12.5 + - - -
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Residues in contact with VAL 72 (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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19A VAL* 3.7 26.2 - - + -
20A VAL 2.8 8.4 + - - +
21A VAL* 3.4 16.8 - - + -
22A GLY 3.0 26.2 + - - -
70A SER* 4.8 2.0 - - - +
71A MET* 1.3 68.7 - - - +
73A CYS* 1.3 63.0 + - - +
97A PHE* 3.3 24.2 - - + +
99A TYR* 4.7 3.1 - - + -
131A LEU* 3.9 12.4 - - + +
135A ASP 5.1 0.9 - - - +
136A LEU* 4.1 24.9 - - + -
139A ALA* 4.2 22.2 - - + -
142A VAL* 4.2 4.7 - - + -
143A ILE* 4.9 0.9 - - + -
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Residues in contact with CYS 73 (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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22A GLY 3.1 20.9 - - - +
23A SER 5.1 0.2 - - - -
24A CYS* 3.6 26.9 - - + +
71A MET* 3.9 15.7 - - + -
72A VAL* 1.3 75.6 - - - +
74A LYS* 1.3 62.1 + - - +
75A VAL* 4.7 2.7 - - - -
88A LEU* 4.8 0.2 - - - -
97A PHE 3.1 6.3 + - - -
98A THR* 3.6 36.1 - - - -
99A TYR* 2.8 30.8 + - - -
128A ASN* 5.2 0.2 - - - +
131A LEU* 3.9 11.4 - - - -
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Residues in contact with LYS 74 (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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22A GLY 4.8 0.8 + - - -
24A CYS 5.3 0.2 - - - +
73A CYS* 1.3 77.2 - - - +
75A VAL* 1.3 77.0 + - - +
99A TYR* 3.4 22.9 - - - +
100A GLN 4.2 10.3 - - - -
101A THR* 3.9 14.9 - - + -
127A ALA* 3.5 29.0 - - - +
128A ASN* 3.5 14.7 + - - +
130A LEU* 3.3 34.2 + - + +
131A LEU* 4.0 16.9 - - + +
132A ASN* 4.4 5.5 - - - +
135A ASP* 2.7 33.3 + - - -
155A ILE* 6.3 0.2 - - - +
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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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24A CYS* 4.0 30.5 - - + +
73A CYS* 4.7 0.4 - - - -
74A LYS* 1.3 78.3 - - - +
76A GLY* 1.3 59.2 + - - +
81A GLY* 3.7 21.5 - - - +
84A TYR* 4.5 10.1 - - + -
85A ILE* 4.6 0.2 - - + -
98A THR* 4.0 17.0 - - + -
99A TYR 2.8 17.8 + - - +
100A GLN* 3.1 18.9 - - + +
101A THR* 2.9 27.7 + - - +
106A THR* 3.7 20.0 - - + +
127A ALA* 3.4 9.9 - - - -
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Residues in contact with GLY 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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75A VAL* 1.3 73.5 - - - +
77A LYS* 1.3 58.2 + - - -
78A ASP* 2.8 23.2 + - - -
81A GLY* 3.5 9.0 - - - -
100A GLN* 3.4 19.0 + - - -
101A THR 3.5 8.7 - - - -
104A ALA 3.7 9.9 - - - -
106A THR* 2.8 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
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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