Contacts of the strand formed by residues 69 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 4.0 4.5 - - - +
18B VAL* 3.2 14.8 - - + -
59B CYS* 3.6 17.7 - - - +
62B ALA* 4.0 7.4 - - + -
63B ALA* 3.8 23.1 - - - +
67B ALA* 3.4 22.8 + - + +
68B MET* 1.3 77.8 - - - +
70B SER* 1.3 62.1 + - - +
92B ASP 4.4 3.8 + - - +
93B ILE* 3.5 30.3 - - - +
94B SER* 3.1 25.2 + - - -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.7 18.8 - - - +
18B VAL 3.1 5.7 + - - -
19B VAL* 3.5 6.6 - - - +
20B VAL* 3.0 26.5 + - - +
59B CYS* 4.4 3.8 - - - -
69B THR* 1.3 76.1 - - - +
71B MET* 1.3 62.9 + - - +
72B VAL* 3.8 2.2 + - - +
93B ILE* 4.4 0.2 - - - -
94B SER* 3.6 24.9 + - - +
96B GLU* 4.8 3.3 + - - +
97B PHE* 4.5 12.8 - - - -
142B VAL* 4.3 18.0 - - - +
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Residues in contact with MET 71 (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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20B VAL* 3.6 9.0 - - + -
22B GLY 3.6 41.3 - - - +
23B SER 3.9 4.0 - - - +
24B CYS* 4.3 1.3 - - - -
55B GLY* 3.7 21.5 - - - +
56B ALA* 3.7 7.9 - - - +
59B CYS* 3.8 24.5 - - - -
70B SER* 1.3 72.0 + - - +
72B VAL* 1.3 60.2 + - - +
73B CYS* 3.7 22.4 - - + -
88B LEU* 4.3 14.6 - - + -
93B ILE* 3.8 19.0 - - + +
94B SER 3.1 12.0 + - - +
97B PHE* 3.5 9.9 + - - +
98B THR* 3.0 22.8 + - - +
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Residues in contact with VAL 72 (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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19B VAL* 4.0 18.2 - - + -
20B VAL 2.8 9.1 + - - +
21B VAL* 3.5 22.6 - - + -
22B GLY 3.1 25.5 + - - -
70B SER* 4.7 2.9 - - - +
71B MET* 1.3 71.8 - - - +
73B CYS* 1.3 64.0 + - - +
97B PHE* 3.3 29.8 - - + +
99B TYR* 4.7 3.8 - - + -
131B LEU* 3.8 15.8 - - + +
135B ASP 5.0 2.2 - - - +
136B LEU* 4.2 22.4 - - + -
139B ALA* 4.4 16.4 - - + -
142B VAL* 5.6 1.3 - - + -
143B ILE* 5.3 0.7 - - + -
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Residues in contact with CYS 73 (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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22B GLY 3.2 18.8 - - - +
24B CYS* 3.5 29.8 - - + +
71B MET* 3.7 16.2 - - + -
72B VAL* 1.3 76.8 - - - +
74B LYS* 1.3 64.6 + - - +
75B VAL* 4.8 1.8 - - - -
88B LEU* 4.6 0.7 - - - -
97B PHE 3.2 5.5 + - - +
98B THR* 3.5 34.1 - - - -
99B TYR* 2.9 28.1 + - - -
128B ASN* 5.3 0.2 - - - +
131B LEU* 3.9 10.3 - - - -
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Residues in contact with LYS 74 (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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22B GLY 4.8 0.8 + - - -
24B CYS* 5.0 0.7 - - - +
73B CYS* 1.3 77.3 - - - +
75B VAL* 1.3 79.4 + - - +
99B TYR* 3.5 26.0 - - + +
100B GLN 5.3 0.9 - - - +
101B THR* 3.7 25.0 - - + -
127B ALA* 3.4 17.2 - - - +
128B ASN* 3.7 27.6 + - - +
130B LEU* 2.9 29.1 + - + +
131B LEU* 4.1 12.9 - - + +
132B ASN* 4.0 6.3 - - - +
135B ASP* 2.9 34.1 + - - -
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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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24B CYS* 3.8 30.5 - - + -
73B CYS* 4.8 4.5 - - - -
74B LYS* 1.3 78.2 - - - +
76B GLY* 1.3 60.9 + - - +
81B GLY* 3.7 25.6 - - - +
84B TYR* 4.3 11.7 - - + -
85B ILE* 4.2 8.5 - - + -
98B THR* 4.5 4.0 - - + -
99B TYR 2.9 19.0 + - - +
100B GLN* 3.3 18.9 - - + -
101B THR* 2.9 28.2 + - - +
106B THR* 4.0 14.4 - - + +
127B ALA* 3.5 8.5 - - - -
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Residues in contact with GLY 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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75B VAL* 1.3 75.3 - - - +
77B LYS* 1.3 58.2 + - - -
78B ASP* 2.8 17.7 + - - -
81B GLY* 3.6 8.7 - - - -
100B GLN* 3.2 15.6 + - - -
101B THR 3.4 9.9 - - - -
104B ALA 3.5 15.3 - - - -
106B THR* 3.0 21.7 + - - +
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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