Contacts of the strand formed by residues 151 - 157 (chain A) in PDB entry 3PHW
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 HIS 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLN 3.6 19.5 + - - -
35A PRO 3.9 11.2 - - - -
36A GLY* 4.1 0.9 - - - -
40A CYS* 3.9 15.6 - - + -
145A LEU 3.4 0.5 - - - +
146A HIS* 3.2 9.5 + - - -
147A SER* 2.9 37.4 + - - +
149A GLN 3.9 0.2 - - - -
150A THR* 1.3 80.5 - - - +
152A PHE* 1.3 73.6 + - - +
153A ASP* 2.9 30.7 + - - -
75B GLY* 3.9 1.8 - - - -
31H GLN* 3.3 24.9 + - - -
37H PRO* 3.5 21.8 - - + -
38H PRO* 3.8 10.1 - - + +
39H ASP* 2.7 25.4 + - - -
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Residues in contact with PHE 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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34A GLN* 3.9 2.3 - - - +
40A CYS* 3.5 14.2 - - - +
41A PHE* 3.7 45.1 - + + +
44A SER* 3.3 16.7 + - - +
100A GLY 4.0 2.9 - - - -
101A SER* 4.4 3.1 - - - -
118A ILE* 4.0 21.5 - - + -
144A LEU* 3.9 18.8 - - + -
145A LEU 3.2 5.6 - - - -
146A HIS* 3.5 34.3 - + + -
151A HIS* 1.3 81.9 + - - +
153A ASP* 1.3 69.6 - - - +
73B LEU* 4.0 16.4 - - + -
74B ARG 3.6 1.3 - - - -
75B GLY* 3.2 37.0 - - - -
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Residues in contact with ASP 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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31A ILE* 4.0 14.4 - - + -
32A VAL 3.8 7.2 - - - +
33A ARG* 2.8 37.5 + - - -
34A GLN* 3.0 21.0 + - - +
44A SER* 3.1 11.3 + - - -
144A LEU* 3.5 7.6 - - - +
145A LEU* 2.9 38.6 + - + +
147A SER* 4.5 3.1 + - - -
151A HIS* 2.9 24.5 + - - -
152A PHE* 1.3 73.0 - - - +
154A ALA* 1.3 60.3 + - - +
31H GLN* 3.3 7.1 + - - -
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Residues in contact with ALA 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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31A ILE* 3.6 5.0 - - - +
32A VAL* 2.8 40.6 + - + +
34A GLN* 4.1 2.2 - - - +
44A SER* 3.5 15.5 + - - +
47A GLU* 3.9 22.9 - - + -
48A LEU* 3.9 24.5 - - + -
143A ASN 4.0 3.1 - - - -
153A ASP* 1.3 75.1 - - - +
155A LEU* 1.3 61.3 + - - +
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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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25A ILE* 3.9 15.9 - - + -
29A PHE* 3.7 23.3 - - + -
30A GLU 3.4 4.0 - - - +
31A ILE* 3.6 33.2 - - + -
48A LEU* 3.5 16.0 - - - +
119A TRP* 3.7 20.2 - - + -
143A ASN* 2.9 28.9 + - + +
144A LEU 3.7 22.7 - - - +
145A LEU* 3.8 24.9 - - + +
154A ALA* 1.3 78.8 - - - +
156A ARG* 1.3 62.8 + - - +
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Residues in contact with ARG 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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29A PHE* 3.2 4.1 - - - -
30A GLU* 2.8 59.1 + - - +
32A VAL* 4.4 16.5 - - + +
47A GLU* 3.2 47.3 + - - +
48A LEU* 3.5 30.7 + - + +
155A LEU* 1.3 71.0 - - - +
157A ILE* 1.3 66.9 + - - +
158A LEU 3.2 0.2 + - - -
162A GLU* 5.5 4.3 - - - +
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.4 8.3 - - + -
28A TYR 3.5 9.2 - - - +
29A PHE* 3.4 21.9 - - + -
138A VAL* 3.8 30.1 - - + +
139A PHE* 3.9 29.8 - - + +
143A ASN* 4.7 4.0 - - - +
156A ARG* 1.3 74.2 - - - +
158A LEU* 1.3 76.9 + - - +
159A PRO* 3.4 2.3 - - - +
161A PHE* 3.8 22.2 - - + +
162A GLU* 2.9 35.6 + - + +
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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