Contacts of the strand formed by residues 59 - 66 (chain U) in PDB entry 1Q82
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 GLU 59 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47U THR* 3.7 10.2 - - + +
48U VAL 3.3 8.5 - - - +
49U GLU* 3.3 39.0 - - + +
50U VAL* 5.7 0.2 - - - -
57U GLY 3.8 2.9 + - - +
58U GLU* 1.3 77.5 - - - +
60U GLY* 1.3 58.9 + - - +
74U VAL* 4.9 2.9 - - - -
75U GLU 4.5 4.9 - - - +
76U ASP* 5.5 3.3 - - - +
77U VAL* 6.0 1.1 - - - +
99U THR* 3.6 21.3 + - - +
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Residues in contact with GLY 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U THR* 4.4 7.5 - - - +
48U VAL* 2.8 35.0 + - - +
59U GLU* 1.3 77.1 - - - +
61U GLU* 1.3 61.1 + - - -
62U VAL 3.9 0.2 + - - -
74U VAL* 3.7 16.3 - - - +
75U GLU* 4.1 9.0 - - - -
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Residues in contact with GLU 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U ALA 4.5 5.4 - - - +
45U GLY* 4.0 14.4 - - - +
46U ASP 3.7 9.6 - - - +
47U THR* 4.2 9.9 - - - +
60U GLY* 1.3 72.0 - - - -
62U VAL* 1.3 74.3 + - - +
63U ILE* 3.1 14.9 + - + +
74U VAL* 4.3 0.9 - - - -
75U GLU* 3.0 44.6 + - - +
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Residues in contact with VAL 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U VAL* 3.6 24.7 - - + -
43U ASN 3.4 20.6 - - - +
44U ALA* 2.6 38.6 - - - +
46U ASP 2.9 20.5 + - - +
48U VAL* 4.1 19.1 - - + -
61U GLU* 1.3 73.4 - - - +
63U ILE* 1.3 58.9 + - - +
64U ASN 3.9 18.4 - - - +
65U VAL* 3.9 8.5 - - + -
72U ILE* 4.4 6.5 - - + -
73U HIS 3.6 6.7 - - - +
74U VAL* 4.3 11.2 - - + +
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Residues in contact with ILE 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U ALA* 4.3 8.4 - - - +
61U GLU* 3.3 33.0 - - + +
62U VAL* 1.3 75.6 - - - +
64U ASN* 1.3 61.8 + - + +
73U HIS* 2.7 20.0 + - + +
74U VAL 4.1 0.9 - - - -
75U GLU* 3.4 39.5 - - + +
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Residues in contact with ASN 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A G 5.5 1.0 + - - -
82A C 5.6 1.0 + - - -
44U ALA* 4.5 4.9 - - - -
62U VAL* 3.6 2.5 - - - +
63U ILE* 1.3 83.8 - - + +
65U VAL* 1.3 84.8 + - - +
66U ASP* 4.2 11.3 + - - +
71U VAL 5.5 0.2 + - - -
72U ILE* 3.3 5.7 - - - +
73U HIS* 2.9 56.6 + - + -
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Residues in contact with VAL 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A G 3.3 41.9 + - - +
82A C 3.6 8.3 + - - -
23U VAL* 4.1 27.6 - - + -
41U ARG* 3.8 18.6 - - - +
42U VAL 3.8 17.7 - - - +
44U ALA 4.0 2.5 - - - +
62U VAL* 3.9 14.1 - - + -
64U ASN* 1.3 88.8 + - - +
66U ASP* 1.3 64.2 + - - +
67U LEU* 3.7 2.0 + - + +
71U VAL 3.7 2.2 - - - -
72U ILE* 3.9 15.9 - - + -
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Residues in contact with ASP 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A C 4.2 6.7 + - - -
23U VAL* 4.2 1.4 - - - +
64U ASN* 4.2 11.7 + - - +
65U VAL* 1.3 75.0 - - - +
67U LEU* 1.3 53.2 + - - +
68U ASP* 3.0 12.0 + - - +
69U LYS* 2.7 46.9 + - + +
70U ALA* 2.8 27.5 + - - -
71U VAL* 2.8 24.8 + - + +
73U HIS* 6.0 3.6 - - + -
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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