Contacts of the helix formed by residues 97 - 106 (chain L) in PDB entry 2B4X
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 ASP 97 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96L ASN* 1.3 74.7 - - + +
98L THR* 1.3 59.1 + - - +
99L LEU* 3.1 2.7 - - - +
100L GLN* 3.1 21.6 + - - +
101L GLN* 2.8 40.8 + - - +
342L ASP* 3.2 25.6 - - - +
350L LYS* 5.7 0.2 - - + -
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Residues in contact with THR 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ALA* 4.5 4.7 - - + -
95L CYS 3.6 9.8 + - - -
96L ASN 2.7 8.1 + - - -
97L ASP* 1.3 73.1 - - - +
99L LEU* 1.3 62.5 + - - +
101L GLN* 4.0 3.2 - - + +
102L LEU* 3.1 31.3 + - + +
340L LEU* 5.8 0.9 - - + -
342L ASP* 3.1 24.9 + - - +
343L LEU* 3.5 47.7 + - + +
348L LYS 3.7 0.5 + - - -
350L LYS* 3.2 27.7 + - - +
351L LEU* 4.8 0.2 - - + -
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Residues in contact with LEU 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L CYS* 3.0 44.0 - - + +
22L ILE 4.0 1.1 - - - +
23L TYR* 3.8 22.0 - - + +
91L LYS* 3.7 44.9 - - + +
94L ALA* 4.3 8.5 - - - +
95L CYS* 3.5 22.4 + - - +
96L ASN* 3.8 4.3 - - - +
97L ASP 3.1 0.6 - - - -
98L THR* 1.3 80.7 - - - +
100L GLN* 1.3 58.7 + - - +
102L LEU* 4.0 2.2 - - - +
103L MET* 3.1 20.1 + - - +
116L SER* 3.9 9.9 - - - +
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Residues in contact with GLN 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 3.3 45.4 - - + +
97L ASP* 3.1 24.7 + - - +
99L LEU* 1.3 77.6 - - - +
101L GLN* 1.3 72.2 + - - +
102L LEU 3.1 1.3 - - - -
103L MET* 2.7 17.8 + - - +
104L GLU* 2.8 45.0 + - - +
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Residues in contact with GLN 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L ASP* 2.8 27.9 + - - +
98L THR* 4.0 4.5 - - - +
100L GLN* 1.3 77.9 - - - +
102L LEU* 1.3 56.8 + - - +
104L GLU* 3.0 15.3 + - - +
105L VAL* 2.8 36.7 + - - +
339L GLY 2.9 14.8 - - - +
340L LEU* 3.7 11.6 - - + +
341L VAL* 2.7 40.8 + - - +
342L ASP* 2.8 39.6 + - - +
343L LEU 6.3 0.2 - - - +
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Residues in contact with LEU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PHE* 3.9 31.0 - - + +
90L THR 4.7 0.9 - - - -
91L LYS* 3.7 31.0 - - + +
94L ALA* 3.5 32.5 - - + -
98L THR* 3.1 26.0 + - + +
99L LEU 4.0 0.7 - - - +
101L GLN* 1.3 76.5 - - - +
103L MET* 1.3 64.0 + - - +
104L GLU 3.2 0.5 + - - -
106L PHE* 3.4 35.5 + - + +
108L PHE* 3.8 4.7 - - + -
340L LEU* 3.4 23.8 - - + -
343L LEU* 4.3 11.4 - - + -
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Residues in contact with MET 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 4.1 23.6 - - + -
25L SER* 5.2 3.4 - - - +
91L LYS* 4.0 23.1 - - + -
99L LEU 3.1 18.3 + - - +
100L GLN* 2.7 13.3 + - - +
102L LEU* 1.3 79.2 - - - +
104L GLU* 1.3 57.5 + - + +
108L PHE* 2.8 63.2 + - - +
109L ASP* 3.0 17.2 + - + +
113L GLU 5.8 1.3 - - - +
114L LYS 5.7 0.7 - - - -
115L THR 4.7 1.6 - - - +
116L SER* 3.6 40.6 - - - +
119L ILE* 4.1 10.1 - - + -
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Residues in contact with GLU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 4.3 6.8 + - - +
100L GLN* 2.8 50.8 + - + +
101L GLN* 3.6 15.2 - - - +
103L MET* 1.3 77.8 - - + +
105L VAL* 1.3 57.6 + - + +
106L PHE 3.0 4.0 - - - -
107L LYS* 2.6 28.8 + - - +
109L ASP* 4.1 18.7 - - + +
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Residues in contact with VAL 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L PHE* 3.1 18.3 - - + +
101L GLN* 2.8 19.9 + - - +
104L GLU* 1.3 72.3 - - + +
106L PHE* 1.3 66.7 + - + +
107L LYS* 3.2 1.8 + - - +
335L LEU* 4.0 22.7 - - + +
338L MET* 3.6 43.3 - - + +
339L GLY* 3.8 3.8 - - - -
340L LEU* 3.5 31.9 - - + +
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Residues in contact with PHE 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L ALA* 4.1 8.0 - - - +
55L ASN* 4.6 2.6 + - - -
58L PHE* 3.5 33.5 - + - +
83L ILE* 3.9 9.0 - - + -
84L SER* 3.7 25.8 - - - +
87L PHE* 3.6 43.1 - + + -
102L LEU* 3.4 19.6 + - + +
104L GLU 3.0 0.8 - - - -
105L VAL* 1.3 82.0 - - + +
107L LYS* 1.3 68.8 - - - +
108L PHE* 2.8 39.2 + + + -
335L LEU* 3.5 31.9 - - + -
340L LEU* 4.2 9.2 - - + -
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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