Contacts of the strand formed by residues 70 - 75 (chain I) in PDB entry 1V7M
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 PHE 70 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ARG* 4.2 8.1 - - - -
48I VAL* 4.2 10.3 - - + -
62I TYR* 3.5 18.5 - - + -
66I VAL* 3.1 49.1 + - + +
68I GLY* 4.7 3.6 + - - -
69I ARG* 1.3 96.5 + - + +
71I THR* 1.3 68.1 + - - +
83I LEU* 4.3 12.3 - - + -
84I GLN 3.1 5.4 - - - +
85I MET* 3.4 45.8 - - + -
86I ASN 3.7 13.9 - - - -
88I LEU* 3.7 16.8 - - + -
92I ASP* 3.9 15.7 - - + -
96I TYR* 4.4 7.6 - + - -
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Residues in contact with THR 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I TYR* 3.2 11.9 - - + +
68I GLY* 6.3 1.6 - - - -
69I ARG 4.5 0.9 + - - -
70I PHE* 1.3 79.7 - - - +
72I VAL* 1.3 62.7 + - - +
73I SER* 4.2 2.8 + - - -
82I TYR 4.0 0.2 - - - +
83I LEU* 3.5 5.9 - - - +
84I GLN* 2.7 53.7 + - - +
86I ASN* 5.2 9.0 - - - +
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Residues in contact with VAL 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I TRP* 4.0 18.8 - - + +
49I ALA* 4.1 17.5 - - + +
50I GLU 4.6 2.2 - - - +
51I ILE* 4.0 28.3 - - + +
60I ILE* 3.5 41.6 - - + +
62I TYR* 3.1 25.4 + - + -
71I THR* 1.3 75.1 - - - +
73I SER* 1.3 67.3 + - - +
81I VAL* 4.5 0.2 - - + -
82I TYR 3.4 12.8 - - - +
83I LEU* 4.5 4.5 - - + -
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Residues in contact with SER 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LYS* 5.0 3.1 + - - -
51I ILE* 4.3 9.0 - - - -
60I ILE* 5.5 0.2 - - - -
71I THR* 4.2 3.4 + - - -
72I VAL* 1.3 76.3 - - - +
74I ARG* 1.3 61.2 - - - +
81I VAL* 3.4 7.0 - - - +
82I TYR* 2.5 58.9 + - - +
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Residues in contact with ARG 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE* 2.8 47.5 + - + -
30I SER* 3.9 4.2 - - - +
32I ALA 2.9 23.6 + - - -
34I MET* 3.9 7.1 - - - +
51I ILE* 3.4 28.6 + - + +
52I ARG 3.2 18.1 + - - -
53I SER* 4.2 4.7 - - - -
58I HIS* 3.4 31.2 + - + +
73I SER* 1.3 80.1 - - - +
75I ASP* 1.3 60.1 + - - +
76I ASP* 2.8 26.6 + - - +
80I SER 3.2 15.3 - - - +
81I VAL* 4.1 8.1 - - + +
82I TYR* 4.4 6.2 - - - -
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Residues in contact with ASP 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I ARG* 1.3 72.6 - - - +
76I ASP* 1.3 66.8 + - - +
77I SER* 2.7 30.5 + - - -
78I LYS* 3.2 23.3 + - + +
79I SER 3.4 6.9 + - - -
80I SER 2.9 15.8 + - - +
82I TYR* 4.0 23.5 + - + +
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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