Contacts of the strand formed by residues 142 - 147 (chain C) 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 VAL 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.8 10.3 - - + -
48C LEU* 3.6 32.3 - - + +
49C THR* 3.6 29.2 - - + -
114C ILE* 3.7 22.0 - - + -
115C THR 2.7 14.3 + - - +
116C ILE* 3.5 12.6 - - + +
117C ILE 3.0 22.8 + - - +
140C THR 5.3 1.6 - - - +
141C ALA* 1.3 73.6 - - - +
143C ASN* 1.3 57.4 + - - +
144C LEU* 3.8 13.9 + - + -
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Residues in contact with ASN 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.9 16.6 - - + -
48C LEU* 3.1 14.3 - - - +
117C ILE* 3.6 20.8 - - - +
119C TRP* 2.9 27.7 + - + -
138C VAL* 3.3 26.9 + - - +
141C ALA* 3.4 11.7 + - - +
142C VAL* 1.3 72.7 - - - +
144C LEU* 1.3 57.4 + - - +
155C LEU* 2.8 51.3 + - + +
157C ILE* 4.7 4.0 - - - +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.8 35.0 - - + -
44C SER* 3.9 30.5 - - - -
45C ILE* 4.1 11.9 - - + +
48C LEU* 4.1 4.7 - - + -
116C ILE* 4.4 13.5 - - + -
117C ILE 2.9 11.5 + - - +
118C ILE* 4.4 8.3 - - + -
119C TRP* 2.7 36.0 + - - +
142C VAL* 3.8 22.2 - - + +
143C ASN* 1.3 83.0 - - - +
145C LEU* 1.3 55.7 + - - +
152C PHE* 4.4 13.5 - - + -
153C ASP 3.5 3.4 - - - +
154C ALA* 4.7 0.2 - - - -
155C LEU* 4.1 3.8 - - - -
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.9 22.2 - - + -
31C ILE* 3.9 36.3 - - + -
33C ARG* 4.2 12.1 - - - +
119C TRP 3.5 7.4 - - - +
121C VAL* 3.5 41.1 - - + -
125C ASP* 6.4 1.1 - - - -
144C LEU* 1.3 70.6 - - - +
146C HIS* 1.3 60.3 + - - +
147C SER* 3.9 5.9 + - - -
151C HIS 3.3 1.4 - - - +
152C PHE* 3.2 8.1 - - - -
153C ASP* 2.9 45.3 + - + +
155C LEU* 3.9 16.9 - - + +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ILE* 3.8 22.2 - - + -
119C TRP 2.8 12.0 + - - +
120C THR* 2.9 24.6 - - - +
121C VAL* 3.1 27.6 + - - +
144C LEU 4.0 0.8 + - - -
145C LEU* 1.3 72.5 - - - +
147C SER* 1.3 58.2 + - - +
149C GLN* 3.4 42.8 + - - -
150C THR 3.8 1.6 - - - -
151C HIS 3.2 12.6 + - - -
152C PHE* 3.7 18.0 - + + -
73D LEU* 3.7 17.6 - - + +
74D ARG 3.0 36.8 - - - -
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 5.0 2.5 + - - -
121C VAL* 3.9 19.3 - - - -
145C LEU* 4.9 9.3 + - - -
146C HIS* 1.3 74.6 - - - +
148C GLY* 1.3 58.8 + - - +
149C GLN 2.9 10.9 + - - +
150C THR 2.9 12.8 + - - -
151C HIS* 2.8 35.3 + - - +
153C ASP* 4.5 3.5 + - - -
31F GLN* 4.2 13.5 + - - -
35F GLY 4.7 7.9 + - - -
37F PRO* 4.0 4.6 - - - +
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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