Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 3VF1
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 ILE 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.9 15.9 - - + -
26A THR 3.5 13.7 - - - +
27A GLY* 4.2 1.1 - - - -
28A LYS* 5.7 0.2 - - - -
61A VAL* 4.0 15.7 - - + -
63A GLU* 1.3 69.8 - - - +
65A ALA* 1.3 61.4 + - - +
66A MET 3.4 23.8 - - - +
67A ILE* 4.3 4.5 - - + -
87A ILE* 3.5 37.2 - - + -
89A LYS* 4.0 21.3 - - + -
100A TYR* 3.3 33.2 - - + -
102A PHE* 3.5 18.6 - - + -
116A GLU* 4.0 10.0 - - - +
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Residues in contact with ALA 65 (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 THR 2.9 8.7 + - - +
27A GLY 4.2 2.5 - - - +
28A LYS* 3.9 27.8 - - + -
63A GLU 3.4 1.8 + - - -
64A ILE* 1.3 74.1 - - - +
66A MET* 1.3 67.1 + - + +
102A PHE* 4.2 0.2 - - - -
115A TYR* 3.7 2.6 - - - +
116A GLU* 2.9 29.3 + - - +
130A THR* 4.7 3.6 - - + -
131A ILE* 4.0 25.6 - - + +
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Residues in contact with MET 66 (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 THR* 3.1 43.8 + - + +
64A ILE* 3.4 6.9 - - - +
65A ALA* 1.3 81.7 - - + +
67A ILE* 1.3 66.2 + - - +
68A THR* 5.5 1.6 - - - +
102A PHE* 3.7 4.0 - - - -
113A VAL* 4.0 12.8 - - + -
114A VAL 3.3 16.4 - - - +
115A TYR* 4.0 11.9 - - + -
130A THR* 3.8 30.1 - - - +
131A ILE* 3.5 31.0 - - + -
134A GLN* 3.8 31.4 - - + -
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Residues in contact with ILE 67 (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 ILE* 4.1 16.6 - - + -
24A LYS 3.6 8.1 - - - +
25A LEU* 4.0 6.5 - - + -
64A ILE* 4.3 0.4 - - + -
66A MET* 1.3 79.2 - - - +
68A THR* 1.3 65.3 + - - +
69A LEU* 4.3 13.0 - - + -
85A VAL* 3.9 33.9 - - + -
87A ILE* 3.7 19.1 - - + -
102A PHE* 3.6 33.0 - - + -
112A LEU 4.0 0.2 - - - +
113A VAL* 3.4 6.7 - - - +
114A VAL* 2.9 50.8 + - + +
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Residues in contact with THR 68 (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 SER 3.4 1.0 - - - +
23A ILE* 3.2 7.6 - - - +
24A LYS* 3.0 57.7 + - - +
26A THR* 4.9 4.7 + - - -
66A MET* 5.5 1.9 - - - +
67A ILE* 1.3 77.7 + - - +
69A LEU* 1.3 66.0 + - - +
70A LYS* 5.8 2.0 - - + -
111A GLN* 3.6 36.3 - - + +
112A LEU 3.6 6.3 - - - +
113A VAL* 4.2 12.8 - - + +
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Residues in contact with LEU 69 (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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21A VAL* 4.2 15.5 - - + -
22A SER 3.3 11.9 - - - +
23A ILE* 3.9 27.4 - - + -
38A LEU* 4.7 4.0 - - + -
67A ILE* 4.3 18.8 - - + -
68A THR* 1.3 77.3 - - - +
70A LYS* 1.3 61.0 + - - +
82A ILE* 4.0 25.4 - - + -
85A VAL* 4.8 7.2 - - + -
104A CYS* 5.1 2.5 - - - -
108A VAL* 4.4 18.7 - - + +
110A LYS 3.8 0.2 - - - +
111A GLN* 3.2 7.3 - - - +
112A LEU* 2.7 58.4 + - + +
114A VAL* 4.5 5.4 - - + -
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Residues in contact with LYS 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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21A VAL* 3.2 7.0 - - - +
22A SER* 2.9 44.3 + - - +
68A THR* 5.8 2.2 - - + -
69A LEU* 1.3 77.5 - - - +
71A GLU* 1.3 92.3 + - - +
72A ASN 3.1 0.3 + - - -
108A VAL* 5.6 0.4 - - - -
110A LYS* 3.3 32.8 + - - +
111A GLN* 4.2 19.8 + - + +
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Residues in contact with GLU 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 SER 4.2 0.9 - - - +
21A VAL* 4.2 9.4 - - - +
70A LYS* 1.3 98.2 + - - +
72A ASN* 1.3 57.6 + - - +
73A GLY* 3.4 22.9 + - - +
77A LYS* 4.1 21.9 - - + +
108A VAL* 5.2 5.0 - - + +
109A ILE 3.3 24.9 - - - +
110A LYS* 3.1 11.6 + - - +
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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