Contacts of the strand formed by residues 107 - 112 (chain E) in PDB entry 1Q57
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 GLN 107 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LEU* 3.2 19.1 - - + +
84E ARG* 5.7 1.0 - - - +
96E TYR* 2.9 48.3 + - + +
97E TRP 3.8 5.2 - - - +
98E ILE* 4.7 9.9 - - + +
105E MET 4.2 0.2 + - - -
106E TYR* 1.3 71.8 - - - +
108E VAL* 1.3 59.2 + - - +
122E LYS 3.6 2.9 - - - +
123E VAL* 3.3 2.6 - - - -
124E ARG* 2.8 87.5 + - + +
160E ILE* 4.1 9.1 - - - +
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Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E TRP* 4.0 8.7 - - + -
96E TYR* 3.5 5.5 - - - -
97E TRP* 2.7 75.6 + - + +
99E ALA* 3.8 20.9 - - + -
106E TYR 4.0 3.6 - - - +
107E GLN* 1.3 74.3 - - - +
109E ALA* 1.3 60.2 + - - +
121E GLN* 3.1 44.9 - - + +
122E LYS 3.8 0.4 - - - -
123E VAL* 3.5 20.9 - - + -
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Residues in contact with ALA 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 GLY 3.8 3.6 - - - -
96E TYR* 3.9 19.0 - - + -
107E GLN 4.0 0.2 + - - -
108E VAL* 1.3 71.4 - - - +
110E ASP* 1.3 62.5 + - - +
111E TYR* 3.5 8.8 + - + -
121E GLN* 3.3 9.0 - - - +
122E LYS 2.9 35.1 + - - +
142E PHE* 4.4 5.4 - - + -
159E GLU* 3.3 34.3 - - + +
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Residues in contact with ASP 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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71E PHE* 5.9 0.7 - - - -
78E TYR* 4.8 5.2 + - - -
94E ALA 4.1 3.8 - - - +
95E GLY* 3.0 22.2 + - - +
97E TRP* 3.0 34.3 + - - -
109E ALA* 1.3 68.9 - - - +
111E TYR* 1.3 63.8 + - - +
112E ARG* 3.6 21.6 + - - +
118E ILE* 3.4 28.0 - - + +
120E SER 4.1 2.0 - - - -
121E GLN* 3.1 24.9 + - - +
142E PHE* 3.7 16.6 - - - -
143E GLY 5.3 0.2 + - - -
145E HIS* 4.9 2.1 + - - -
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Residues in contact with TYR 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 ALA* 3.7 14.6 - - + -
110E ASP* 1.3 71.9 - - - +
112E ARG* 1.3 59.7 + - - +
118E ILE* 3.7 2.0 - - - -
119E VAL* 3.0 23.3 + - + +
120E SER* 3.0 31.3 + - - +
122E LYS* 3.8 20.0 + - + +
136E HIS* 3.6 28.7 - + - -
140E ALA* 4.0 8.3 - - + -
141E LEU 3.8 5.2 - - - +
142E PHE* 3.1 47.7 - - + +
143E GLY 5.8 0.2 - - - +
159E GLU* 3.1 39.0 + - - +
177E SER 4.6 0.2 - - - -
178E LEU 3.9 10.9 + - - -
179E GLY* 3.9 16.6 + - - -
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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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78E TYR* 5.1 7.5 + - - -
95E GLY* 5.9 3.8 - - - -
110E ASP* 3.6 20.5 + - - +
111E TYR* 1.3 74.9 - - - +
113E ASP* 1.3 65.1 + - - +
116E GLY 3.1 25.2 + - - +
117E ASN 3.0 20.6 - - - +
118E ILE* 3.2 36.4 - - - +
119E VAL* 4.1 2.2 - - - -
141E LEU 4.4 6.9 + - - +
143E GLY 5.9 0.6 - - - +
144E LYS* 4.3 6.6 - - - +
145E HIS* 3.1 57.0 + - + +
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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