Contacts of the strand formed by residues 116 - 120 (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 ILE 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.0 24.7 - - + -
105C ALA* 3.6 42.2 - - + +
108C LEU* 4.2 3.4 - - + -
109C ALA* 4.1 9.4 - - + +
114C ILE* 3.5 32.1 - - + -
115C THR* 1.3 72.1 - - - +
117C ILE* 1.3 70.6 + - - +
118C ILE* 4.4 3.1 - - + -
132C LYS* 3.5 1.4 - - - +
133C PHE* 2.8 43.3 + - + +
142C VAL* 3.5 14.4 - - + +
144C LEU* 4.4 16.4 - - + -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TRP* 4.0 17.7 - - + -
115C THR 4.2 0.2 - - - -
116C ILE* 1.3 77.4 - - - +
118C ILE* 1.3 65.3 + - - +
119C TRP* 3.4 32.9 + - + +
131C ILE 3.4 9.4 - - - +
132C LYS* 3.7 30.1 - - + -
138C VAL* 3.6 32.1 - - + -
141C ALA* 3.7 11.4 - - + -
142C VAL 3.0 8.3 + - - +
143C ASN* 3.6 20.2 - - - +
144C LEU* 2.9 28.9 + - - +
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Residues in contact with ILE 118 (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* 4.8 3.6 - - + -
102C THR* 3.7 28.9 - - + +
105C ALA* 4.2 16.6 - - + -
116C ILE* 4.4 11.9 - - + -
117C ILE* 1.3 77.2 - - - +
119C TRP* 1.3 61.8 + - - +
120C THR* 3.7 1.9 + - - -
129C ALA 3.8 0.2 - - - +
130C GLY* 3.5 2.8 - - - -
131C ILE* 2.9 39.0 + - + +
133C PHE* 4.4 5.4 - - + -
144C LEU* 3.6 12.1 - - + +
146C HIS* 3.8 26.7 - - + -
152C PHE* 3.8 24.0 - - + -
73D LEU* 4.1 15.9 - - + +
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Residues in contact with TRP 119 (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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4C LEU* 6.3 0.9 - - + -
7C LEU* 4.3 18.2 - - + -
9C TRP* 4.2 13.9 - + - -
19C SER* 4.1 8.7 - - - -
21C PRO* 3.6 34.1 - - + -
23C PHE* 4.1 13.9 - + - -
25C ILE* 4.0 19.1 - - + -
29C PHE* 3.9 11.0 - + - -
117C ILE* 3.4 19.1 - - + +
118C ILE* 1.3 70.2 - - - +
120C THR* 1.3 60.0 + - - +
121C VAL* 4.7 0.2 - - - -
127C VAL* 3.7 16.6 - - + -
129C ALA 3.7 2.0 - - - -
130C GLY* 3.6 25.1 - - - -
138C VAL* 4.4 9.6 - - + -
143C ASN* 2.9 28.3 + - + -
144C LEU 2.7 14.8 + - - +
145C LEU* 3.5 7.2 - - - +
146C HIS 2.8 25.6 + - - -
155C LEU* 3.8 21.8 - - + -
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Residues in contact with THR 120 (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 3.7 1.8 + - - -
119C TRP* 1.3 73.4 - - - +
121C VAL* 1.3 61.2 + - - +
127C VAL* 3.8 1.2 - - - +
128C GLU* 2.9 35.8 + - + +
129C ALA* 3.0 35.0 + - + +
131C ILE* 6.4 0.9 - - + -
146C HIS* 2.9 35.1 + - - -
149C GLN* 4.1 7.0 + - - +
8D LEU* 4.8 10.3 - - + -
73D LEU* 4.1 16.9 - - + +
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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