Contacts of the strand formed by residues 148 - 156 (chain A) in PDB entry 3Q2U
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A MET* 4.4 2.3 - - - +
59A THR* 2.8 33.0 + - - +
60A TRP 4.0 6.4 + - - +
61A ASP* 4.0 19.5 - - + +
64A LEU* 3.6 17.5 - - + -
93A PHE* 3.8 22.4 - - + -
146A SER 3.8 0.2 - - - -
147A TYR* 1.3 94.9 + - + +
149A VAL* 1.3 60.8 + - - +
175A TYR* 3.3 8.1 - - - +
176A GLY 2.9 30.5 + - - +
211A ARG 3.0 21.1 + - - -
213A GLN 2.9 28.5 + - - -
214A VAL* 4.7 0.4 - - - +
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Residues in contact with VAL 149 (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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37A CYS 5.0 0.9 - - - +
38A VAL* 4.6 9.2 - - + -
41A HIS* 4.0 12.6 - - + +
58A MET* 3.7 28.7 - - + -
59A THR 2.9 14.4 + - - +
60A TRP* 3.3 15.4 - - + -
61A ASP 2.8 23.7 + - - -
64A LEU* 3.9 3.8 - - - -
148A LYS* 1.3 74.3 - - - +
150A GLY* 1.3 62.0 + - - +
151A CYS* 3.8 21.5 - - - -
173A CYS* 3.8 3.6 - - + -
174A ASN 3.3 12.6 - - - +
175A TYR* 3.7 21.8 - - + -
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Residues in contact with GLY 150 (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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60A TRP* 3.9 8.1 - - - -
61A ASP 3.8 3.1 - - - -
64A LEU* 3.6 5.1 - - - +
65A ALA* 3.6 26.5 - - - -
68A ALA* 3.8 4.9 - - - +
149A VAL* 1.3 76.6 - - - +
151A CYS* 1.3 60.8 + - - -
173A CYS* 3.3 0.5 - - - -
174A ASN* 2.8 34.7 + - - +
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Residues in contact with CYS 151 (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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28A ILE* 3.5 9.0 - - - +
33A PHE* 3.4 15.6 - - + -
37A CYS* 3.8 30.1 - - - -
41A HIS* 4.5 0.4 - - - -
60A TRP* 3.1 11.0 - - + -
65A ALA* 3.7 4.1 - - - +
68A ALA* 4.0 2.9 - - - -
149A VAL* 3.8 11.2 - - - -
150A GLY* 1.3 73.7 - - - -
152A ALA* 1.3 63.9 + - - +
171A PHE* 3.6 14.4 - - + -
172A ILE 3.0 7.9 - - - +
173A CYS* 2.1 48.0 - - - -
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Residues in contact with ALA 152 (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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28A ILE* 3.4 18.6 - - + -
33A PHE* 3.9 4.5 - - - -
68A ALA 3.7 4.9 - - - +
69A LYS* 3.3 39.7 - - + +
72A ALA* 4.5 4.9 - - + +
151A CYS* 1.3 75.7 - - - +
153A VAL* 1.3 62.1 + - - +
170A HIS 3.9 0.7 - - - +
171A PHE* 3.4 6.4 - - - -
172A ILE* 2.8 30.8 + - - +
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Residues in contact with VAL 153 (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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25A LEU* 4.1 14.1 - - + +
26A PRO* 3.5 47.2 + - + +
28A ILE* 5.2 0.2 - - - +
33A PHE* 4.3 5.8 - - + -
72A ALA* 5.0 0.2 - - - -
108A PHE* 4.0 28.0 - - + -
152A ALA* 1.3 77.7 - - - +
154A GLN* 1.3 65.5 + - - +
155A PHE 4.5 0.2 + - - -
169A ALA* 3.9 26.9 - - + -
170A HIS 3.3 11.2 - - - +
171A PHE* 4.0 3.4 - - + -
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Residues in contact with GLN 154 (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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25A LEU* 4.2 4.0 - - - -
69A LYS* 4.8 6.1 - - - +
72A ALA* 3.5 34.8 - - + +
73A SER* 3.6 29.4 + - - +
75A CYS* 3.9 2.2 - - - -
153A VAL* 1.3 77.0 - - - +
155A PHE* 1.3 77.7 + - - +
156A CYS* 3.7 10.8 + - - -
169A ALA* 3.6 4.5 - - - -
170A HIS* 2.8 33.1 + - - +
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Residues in contact with PHE 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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25A LEU* 4.0 14.3 - - + +
75A CYS* 4.3 0.5 - - - -
105A VAL* 3.8 17.3 - - + -
154A GLN* 1.3 89.9 + - - +
156A CYS* 1.3 58.1 + - - +
157A PRO* 3.6 20.0 - - + +
167A ASN* 3.7 50.5 - - + -
168A GLY 3.5 10.5 - - - -
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Residues in contact with CYS 156 (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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75A CYS* 2.0 49.8 - - - -
154A GLN* 3.7 11.4 - - - -
155A PHE* 1.3 73.4 - - - +
157A PRO* 1.3 68.5 - - - +
158A LYS* 3.2 11.9 + - - +
159A VAL* 3.5 13.7 - - + +
165A LEU* 5.7 0.3 - - - +
166A SER* 4.9 0.2 - - - -
167A ASN* 3.3 2.0 + - - -
168A GLY 2.8 38.5 + - - +
170A HIS* 3.6 23.8 - - + -
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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