Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 3QD4
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 LYS 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.6 30.0 - - + +
113A LEU 3.3 8.1 - - - +
114A GLU* 4.3 16.8 - - + +
115A LYS* 4.0 6.1 - - - -
150A GLN* 3.0 8.0 - - - +
151A ASP* 2.7 43.4 + - - +
153A GLU* 1.3 87.5 - - + +
155A LEU* 1.3 60.4 + - - +
156A TYR* 3.6 23.5 - - + +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS 3.5 1.1 - - - +
112A ILE* 3.4 6.8 - - - +
113A LEU* 2.7 53.3 + - + +
115A LYS* 3.9 20.6 - - + +
118A ILE* 5.2 5.2 - - + -
127A VAL* 4.1 26.2 - - + -
149A PHE 3.8 3.6 - - - +
150A GLN* 3.6 37.5 - - + +
154A LYS* 1.3 73.6 - - - +
156A TYR* 1.3 62.6 + - - +
157A PHE* 4.6 12.1 - - + -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.9 12.4 - - + +
84A PHE* 4.3 13.7 - + - -
110A ILE* 3.9 12.6 - - + -
111A LYS 3.3 3.6 - - - -
112A ILE* 3.9 36.1 - - + -
148A THR* 3.1 8.3 - - - -
149A PHE* 2.8 78.6 + + + +
150A GLN* 4.0 0.2 - - - -
151A ASP* 2.7 33.9 + - - -
154A LYS* 3.6 35.1 - - + +
155A LEU* 1.3 75.0 - - - +
157A PHE* 1.3 66.1 + - - +
158A GLY 4.1 0.4 - - - -
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA 3.4 0.2 - - - +
110A ILE* 3.2 7.6 - - - +
111A LYS* 2.8 48.4 + - + -
113A LEU* 4.4 18.8 - - + -
127A VAL* 3.7 37.2 - - + -
130A GLU* 3.9 23.6 - - - -
131A ARG* 4.0 27.1 - - + -
145A LEU* 4.2 14.4 - - + -
147A PHE 3.7 2.7 - - - -
148A THR* 3.9 20.2 - - + -
155A LEU* 4.6 14.4 - - + -
156A TYR* 1.3 81.8 - - - +
158A GLY* 1.3 61.0 + - - +
159A LEU* 3.4 16.1 + - + +
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Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 4.8 2.0 - - - -
109A ALA 4.1 1.8 - - - -
110A ILE* 4.3 6.5 - - - -
145A LEU* 3.5 3.8 - - - -
146A TYR* 2.7 36.7 + - - +
147A PHE* 2.8 47.0 + - - +
157A PHE* 1.3 70.7 - - - +
159A LEU* 1.3 56.3 + - - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 5.0 1.8 - - + -
108A TYR* 3.6 9.2 - - - +
109A ALA* 2.8 37.7 + - + +
111A LYS* 4.3 18.2 - - + +
130A GLU* 5.8 0.4 - - - +
134A MET* 4.3 17.0 - - + -
143A VAL* 3.8 10.3 - - + -
144A LYS 3.2 8.1 - - - +
145A LEU* 4.0 22.9 - - + -
146A TYR* 4.0 4.3 - - - -
157A PHE* 3.8 14.6 - - + +
158A GLY* 1.3 80.4 - - - +
160A SER* 1.3 69.3 + - - +
161A TYR 3.4 0.7 + - - -
360A 3Q6 3.7 43.1 - - + +
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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