Contacts of the strand formed by residues 111 - 115 (chain B) in PDB entry 1QAE
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 ILE 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.5 12.0 - - - +
59B TRP* 3.7 18.6 - - + -
76B TYR* 3.8 12.7 + - + +
87B ARG* 3.5 35.9 - - + +
88B GLY 3.2 2.5 - - - +
89B HIS* 3.6 37.5 - - + +
105B LEU 4.3 2.2 - - - +
107B TYR 3.6 15.3 - - - +
108B LEU* 3.2 33.9 + - + +
109B SER 4.5 2.4 - - - +
110B ASN* 1.3 90.0 - - - +
112B THR* 1.3 83.5 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 17.5 - - + -
76B TYR* 3.4 7.6 - - - -
86B ASP 3.3 0.7 - - - +
88B GLY 3.0 24.0 + - - -
90B GLN* 3.4 33.4 - - + +
111B ILE* 1.3 83.5 - - - +
113B PRO* 1.3 70.6 - - - +
114B GLN* 2.9 11.8 + - - +
148B PRO* 5.2 0.7 - - + -
167B PRO* 4.1 7.9 - - + -
170B TYR* 2.6 38.4 + - + -
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.4 30.7 - - + -
76B TYR* 3.6 11.9 - - + +
85B VAL* 3.9 25.9 - - + +
86B ASP 3.6 7.0 - - - +
112B THR* 1.3 82.9 - - - +
114B GLN* 1.3 60.1 + - - +
157B LEU* 3.9 23.6 - - + -
166B ILE* 3.8 21.5 - - + +
167B PRO* 4.0 6.5 - - + -
170B TYR* 3.4 2.3 + - - -
192B GLN* 3.0 20.6 + - - -
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 3.9 1.8 - - - -
86B ASP* 2.6 34.7 + - - +
88B GLY* 3.7 19.8 - - - -
89B HIS 4.5 1.4 + - - +
112B THR* 2.9 11.5 + - - +
113B PRO* 1.3 72.8 - - - +
115B LYS* 1.3 71.8 + - - +
118B LEU* 4.0 8.2 - - + +
119B ASN* 3.4 35.9 + - + +
123B TRP* 3.9 28.4 + - - +
170B TYR* 3.6 45.1 - - + +
192B GLN* 3.6 1.3 - - - +
251B MG 4.1 1.2 - - - -
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 2.6 38.4 + - - +
84B LYS* 3.6 9.9 - - + +
85B VAL* 4.0 7.2 - - + +
113B PRO 4.0 0.6 + - - -
114B GLN* 1.3 72.0 - - - +
116B SER* 1.3 61.8 + - - +
117B ASP* 4.4 6.3 - - + +
118B LEU* 3.0 6.7 + - + +
119B ASN* 2.9 25.5 + - - +
154B MET* 3.9 18.3 + - - +
192B GLN* 2.8 50.7 + - + +
193B ASN* 3.9 19.1 - - - +
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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