Contacts of the strand formed by residues 107 - 112 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D LEU* 3.2 19.6 - - + +
84D ARG* 5.7 1.8 - - - +
96D TYR* 2.9 50.0 + - + +
97D TRP 3.8 2.7 - - - +
98D ILE* 4.7 12.1 - - + +
105D MET 4.3 0.2 + - - -
106D TYR* 1.3 70.5 - - - +
108D VAL* 1.3 60.5 + - - +
109D ALA 4.0 0.3 + - - -
122D LYS 3.7 2.4 - - - +
123D VAL* 3.4 2.3 - - - -
124D ARG* 2.8 84.6 + - + +
160D ILE* 4.1 8.9 - - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TRP* 4.0 4.0 - - + -
96D TYR* 3.6 5.6 - - - -
97D TRP* 2.7 77.8 + - + +
99D ALA* 3.9 14.8 - - + -
106D TYR 3.9 3.8 - - - +
107D GLN* 1.3 74.4 - - - +
109D ALA* 1.3 59.0 + - - +
121D GLN* 3.2 41.1 - - + +
122D LYS 3.8 0.9 - - - -
123D VAL* 3.4 28.3 - - + -
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLY 3.8 4.0 - - - -
96D TYR* 3.9 19.5 - - + -
107D GLN 4.0 0.2 + - - -
108D VAL* 1.3 71.2 - - - +
110D ASP* 1.3 63.7 + - - +
111D TYR* 3.5 8.4 + - + -
121D GLN* 3.3 7.7 - - - +
122D LYS 2.9 32.7 + - - +
142D PHE* 4.3 4.5 - - + -
159D GLU* 3.2 35.4 - - + +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PHE* 5.9 0.7 - - - -
78D TYR* 4.7 5.4 + - - -
94D ALA 4.2 4.0 - - - +
95D GLY* 3.0 21.5 + - - +
97D TRP* 3.0 25.3 + - - -
109D ALA* 1.3 69.8 - - - +
111D TYR* 1.3 63.5 + - - +
112D ARG* 3.6 22.2 + - - +
118D ILE* 3.4 27.6 - - + +
120D SER 4.1 1.8 - - - -
121D GLN* 3.0 33.8 + - - +
142D PHE* 3.7 16.0 - - - -
143D GLY 5.3 0.5 + - - -
145D HIS* 5.0 1.9 + - - -
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Residues in contact with TYR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ALA* 3.7 15.7 - - + -
110D ASP* 1.3 72.5 - - - +
112D ARG* 1.3 59.8 + - - +
118D ILE* 3.7 2.4 - - - -
119D VAL* 2.9 23.2 + - - +
120D SER* 2.9 32.9 + - - +
122D LYS* 3.9 20.4 + - + +
136D HIS* 3.6 27.8 - + - -
140D ALA* 4.0 8.3 - - + -
141D LEU 3.9 5.8 - - - +
142D PHE* 3.1 45.6 - - + +
143D GLY 5.9 0.2 - - - +
159D GLU* 3.1 39.6 + - - +
178D LEU 3.9 11.5 + - - -
179D GLY* 4.0 15.3 + - - -
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D TYR* 5.0 8.1 + - - -
94D ALA 6.0 0.2 + - - -
95D GLY* 5.8 3.8 - - - -
110D ASP* 3.6 19.9 + - - +
111D TYR* 1.3 75.7 - - - +
113D ASP* 1.3 64.0 + - - +
116D GLY* 3.1 24.9 + - - +
117D ASN 3.1 20.9 - - - +
118D ILE* 3.2 35.1 - - - +
119D VAL* 4.1 1.6 - - - +
141D LEU 4.5 5.0 + - - +
143D GLY 5.9 0.6 - - - +
144D LYS* 4.4 8.5 - - - +
145D HIS* 3.2 56.8 + - + +
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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