Contacts of the strand formed by residues 104 - 112 (chain E) in PDB entry 2H46
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 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E LYS* 3.6 4.0 - - - +
101E PHE 2.9 31.7 + - - +
102E GLY 3.2 1.2 - - - -
103E ASN* 1.3 92.9 - - - +
105E VAL* 1.3 72.1 + - - +
106E GLN* 4.0 14.3 + - + +
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Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLU* 3.8 55.0 - - + +
74E LEU* 4.0 24.5 - - + -
75E SER* 3.9 21.5 - - - +
98E SER* 4.4 0.2 - - - -
99E VAL 3.2 10.1 - - - +
100E LYS* 4.4 3.4 - - + -
104E ASP* 1.3 80.2 - - - +
106E GLN* 1.3 64.1 + - - +
107E HIS* 3.7 22.0 + - + -
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Residues in contact with GLN 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LEU 3.7 0.3 - - - +
98E SER* 3.3 3.6 - - - -
99E VAL* 2.7 38.8 + - + +
101E PHE* 3.9 33.5 + - + +
104E ASP* 4.0 13.4 + - + +
105E VAL* 1.3 77.2 - - - +
107E HIS* 1.3 63.4 + - - +
108E PHE* 3.4 33.3 - - + -
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Residues in contact with HIS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ARG* 3.2 30.9 - - + +
71E GLU* 2.7 43.0 + - + +
86E ARG* 3.5 14.8 + - - +
96E SER* 5.5 2.2 - - - -
97E LEU 3.2 5.6 - - - +
98E SER* 2.7 34.5 + - - -
105E VAL* 3.7 13.9 + - + -
106E GLN* 1.3 73.8 + - - +
108E PHE* 1.3 71.3 + - - +
109E LYS 4.3 0.7 - - - -
169E GOL 4.8 4.9 - - - +
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Residues in contact with PHE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E SER* 3.4 2.8 - - - -
97E LEU* 2.7 53.7 + - + +
99E VAL* 4.4 19.5 - - + -
106E GLN* 3.4 46.4 - - + -
107E HIS* 1.3 80.1 - - - +
109E LYS* 1.3 65.6 + - - +
110E VAL* 3.5 0.7 + - - +
120E LEU* 4.4 24.9 - - + -
121E TRP* 6.3 2.9 - + - -
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Residues in contact with LYS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E PHE 4.0 5.8 - - - +
96E SER* 4.2 10.1 - - - +
107E HIS 4.3 0.2 - - - -
108E PHE* 1.3 75.0 - - - +
110E VAL* 1.3 62.9 + - - +
111E LEU* 3.5 26.8 + - + +
119E PHE 4.2 0.3 - - - +
120E LEU* 3.8 13.9 - - - +
169E GOL 5.6 12.8 - - - +
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Residues in contact with VAL 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ILE* 4.6 12.3 - - + -
94E ASP* 5.0 8.5 - - - +
95E PHE* 2.9 47.3 + - + +
96E SER* 4.1 7.2 - - - +
97E LEU* 4.3 3.8 - - + +
108E PHE 4.3 1.6 - - - +
109E LYS* 1.3 74.9 - - - +
111E LEU* 1.3 64.3 + - - +
112E ARG* 4.7 4.2 - - - +
118E TYR* 3.7 40.6 - - + -
119E PHE 3.9 7.0 - - - +
120E LEU* 4.1 15.7 - - + -
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E LYS* 4.0 27.1 - - + +
110E VAL* 1.3 80.2 - - - +
112E ARG* 1.3 64.8 + - - +
118E TYR* 3.2 5.9 - - - -
119E PHE* 2.8 69.0 + - + +
120E LEU 3.7 13.7 - - - +
121E TRP* 5.5 0.4 - - - -
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Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 5.5 6.1 - - - -
94E ASP* 5.3 9.2 - - - +
95E PHE* 6.1 1.1 - - - -
110E VAL 4.1 4.5 + - - +
111E LEU* 1.3 81.7 - - - +
113E ASP* 1.3 64.5 + - - +
116E GLY* 2.6 41.3 + - - -
117E LYS 3.1 6.7 - - - +
118E TYR* 3.6 36.6 + - + -
119E PHE* 4.0 6.8 - - - -
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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