Contacts of the strand formed by residues 59 - 66 (chain T) in PDB entry 1VQ7
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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47T THR* 3.4 13.5 - - + +
48T VAL 3.3 4.2 - - - +
49T GLU* 3.5 32.5 - - + +
57T GLY 3.8 4.7 + - - +
58T GLU* 1.3 78.3 - - - +
60T GLY* 1.3 57.3 + - - +
74T VAL* 4.9 3.1 - - - -
75T GLU 4.6 4.3 - - - +
76T ASP* 5.7 1.6 - - - +
77T VAL* 6.3 0.7 - - - -
99T THR* 2.8 31.2 + - - +
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Residues in contact with GLY 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T THR* 3.4 7.1 - - - +
48T VAL* 2.8 34.4 + - - +
59T GLU* 1.3 77.8 + - - +
61T GLU* 1.3 63.3 + - - -
62T VAL 3.8 0.3 + - - -
74T VAL* 3.8 17.7 - - - +
75T GLU* 4.3 7.4 - - - -
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Residues in contact with GLU 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ALA 4.5 3.0 - - - +
45T GLY* 3.9 14.1 - - - +
46T ASP 3.6 12.8 - - - +
47T THR* 4.3 7.6 - - - +
60T GLY* 1.3 71.8 - - - -
62T VAL* 1.3 75.9 + - - +
63T ILE* 3.0 15.6 - - + +
74T VAL* 4.4 1.6 - - - -
75T GLU* 2.8 54.0 + - - +
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Residues in contact with VAL 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T VAL* 3.5 26.7 - - + -
43T ASN 3.4 19.1 - - - +
44T ALA* 2.5 30.7 - - - +
46T ASP* 3.0 20.1 + - + +
48T VAL* 4.4 15.9 - - + -
60T GLY 3.8 0.2 + - - -
61T GLU* 1.3 75.7 - - - +
63T ILE* 1.3 58.9 + - - +
64T ASN 3.8 4.0 - - - +
65T VAL* 3.7 25.6 - - + -
72T ILE* 4.3 6.7 - - + -
73T HIS 3.3 13.0 - - - +
74T VAL* 4.3 7.6 - - + +
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Residues in contact with ILE 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ALA* 4.4 8.9 - - - +
61T GLU* 3.0 33.4 - - + +
62T VAL* 1.3 77.5 - - - +
64T ASN* 1.3 61.0 + - + +
73T HIS* 2.6 20.6 + - + +
74T VAL 4.0 1.6 - - - -
75T GLU* 3.4 44.6 - - + +
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Residues in contact with ASN 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810 G 5.5 0.2 - - - -
820 C 5.7 0.9 + - - -
44T ALA* 4.5 4.5 - - - +
62T VAL* 3.6 1.7 - - - +
63T ILE* 1.3 83.9 - - + +
65T VAL* 1.3 74.4 + - - +
66T ASP* 4.0 18.4 + - - +
72T ILE* 3.2 4.5 - - - +
73T HIS* 2.7 64.7 + - + +
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Residues in contact with VAL 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810 G 3.4 40.8 + - - +
820 C 3.7 6.4 + - - -
23T VAL* 4.2 16.8 - - + -
41T ARG* 3.5 26.2 - - - +
42T VAL 3.7 17.0 - - - +
44T ALA 4.0 3.1 - - - +
62T VAL* 3.7 20.0 - - + -
64T ASN* 1.3 87.9 + - - +
66T ASP* 1.3 63.2 + - - +
67T LEU* 3.7 2.8 + - + -
71T VAL 3.6 3.1 - - - -
72T ILE* 3.8 16.6 - - + -
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Residues in contact with ASP 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820 C 4.3 6.8 + - - -
23T VAL* 4.2 1.4 - - - +
64T ASN* 4.0 12.1 + - - +
65T VAL* 1.3 75.1 - - - +
67T LEU* 1.3 58.4 + - - +
68T ASP* 3.0 17.9 + - - +
69T LYS* 2.7 44.8 + - + +
70T ALA* 2.9 22.2 + - - -
71T VAL* 2.8 26.4 + - + +
73T HIS* 6.1 2.5 - - + -
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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