Contacts of the helix formed by residues 72 - 80 (chain K) in PDB entry 1VYJ
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 LEU 72 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16K LEU* 3.6 19.6 - - + +
19K LEU* 4.3 15.7 - - + -
20K LYS* 3.8 10.0 - - + +
23K ILE* 3.3 48.9 - - + +
24K ASN 3.2 11.4 + - - +
25K GLU* 4.1 4.0 - - - -
26K ALA* 4.0 12.8 - - + +
28K TRP* 3.6 31.2 - - + +
37K LEU* 4.8 0.2 - - + -
70K VAL* 3.5 17.7 + - + +
71K ASN* 1.3 71.0 + - - +
73K THR* 1.3 64.6 + - - +
75K MET* 3.9 2.5 - - - -
76K SER* 3.2 23.0 + - - -
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Residues in contact with THR 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K LYS* 4.7 20.8 + - + +
24K ASN* 3.9 11.4 + - - -
71K ASN* 3.0 10.7 + - - -
72K LEU* 1.3 78.7 - - - +
74K SER* 1.3 64.9 + - - +
76K SER* 3.2 7.6 + - - -
77K LYS* 3.0 39.9 + - + +
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Residues in contact with SER 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G LEU* 4.0 32.5 - - - +
71K ASN* 3.2 33.8 + - - +
73K THR* 1.3 77.7 - - - +
75K MET* 1.3 62.5 + - - +
77K LYS* 3.2 7.2 + - - +
78K ILE* 3.1 25.9 + - - +
116K MET* 4.3 13.2 - - - -
117K LYS 6.1 0.2 - - - -
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Residues in contact with MET 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 4.7 1.6 - - + -
16K LEU* 3.4 41.7 - - + -
28K TRP* 4.0 20.6 - - + -
70K VAL* 3.7 29.8 - - + -
71K ASN 3.0 6.7 + - - +
72K LEU 4.1 0.4 - - - +
74K SER* 1.3 72.5 - - - +
76K SER* 1.3 66.3 + - - +
78K ILE* 3.2 5.5 + - - +
79K LEU* 2.8 28.4 + - + +
90K LEU* 4.5 15.0 - - + -
99K LEU* 4.3 9.9 - - + -
101K LEU* 3.9 24.0 - - + -
116K MET* 3.6 24.9 - - - -
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Residues in contact with SER 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K LEU* 3.7 14.7 + - - +
17K GLU* 2.8 26.9 + - - -
20K LYS* 3.5 25.6 + - - +
72K LEU 3.2 20.7 + - - -
73K THR 3.4 5.2 - - - -
75K MET* 1.3 75.1 - - - +
77K LYS* 1.3 66.1 + - - +
79K LEU* 3.0 8.0 + - - +
80K LYS* 2.9 29.9 + - - +
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Residues in contact with LYS 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G HIS* 4.4 29.2 + - + +
154G ILE* 5.6 0.4 - - - -
175G LEU* 3.7 30.4 - - + +
73K THR* 3.0 27.5 + - + +
74K SER* 3.2 8.9 + - - +
76K SER* 1.3 80.0 - - - +
78K ILE* 1.3 62.3 + - - +
80K LYS* 3.1 25.1 + - + +
81K CYS* 3.8 8.9 + - - -
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Residues in contact with ILE 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ILE* 4.2 18.4 - - + +
175G LEU* 4.7 14.6 - - + +
176G GLY 5.6 0.7 - - - +
177G ASN 6.0 0.7 - - - +
74K SER 3.1 19.5 + - - +
75K MET 3.4 7.0 - - - +
77K LYS* 1.3 77.0 - - - +
79K LEU* 1.3 59.4 + - - +
81K CYS* 2.9 32.3 + - - +
101K LEU* 3.7 27.6 - - + -
103K PHE* 3.2 18.4 - - + -
114K TYR* 3.9 20.4 - - + -
115K GLU 5.0 2.5 - - - +
116K MET* 3.9 36.3 - - + +
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Residues in contact with LEU 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 3.4 31.2 - - + +
13K LYS* 3.1 29.2 + - + +
16K LEU* 3.4 38.8 - - + -
75K MET* 2.8 20.7 + - + +
76K SER* 3.0 6.9 + - - +
78K ILE* 1.3 70.2 - - - +
80K LYS* 1.3 56.0 + - - +
81K CYS 2.9 10.1 + - - -
82K ALA* 3.1 9.5 + - - +
88K ILE* 4.2 19.5 - - + -
101K LEU* 4.3 16.4 - - + -
103K PHE* 3.7 27.6 - - + -
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Residues in contact with LYS 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ARG* 5.2 6.1 + - - -
149G ARG* 5.8 0.5 + - - -
150G ASP* 4.2 9.0 - - - +
153G HIS* 5.0 16.6 - - + +
13K LYS* 3.5 17.3 + - - +
17K GLU* 3.5 34.4 + - - +
20K LYS* 5.3 2.5 - - - +
76K SER* 2.9 21.0 + - - +
77K LYS* 3.3 15.3 - - + +
78K ILE 3.1 0.8 - - - -
79K LEU* 1.3 76.6 - - - +
81K CYS* 1.3 59.0 + - - +
82K ALA 3.4 3.9 - - - +
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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