Contacts of the helix formed by residues 135 - 147 (chain C) in PDB entry 3PRJ
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 ARG 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A ASP* 4.7 17.8 + - - -
323A PHE* 4.2 19.1 - - + +
106C LEU* 4.1 6.3 - - + +
133C PRO 3.8 0.8 + - - -
134C VAL* 1.3 78.6 - - + +
136C ALA* 1.3 64.4 + - - +
137C ALA 3.4 2.2 - - - -
138C GLU* 2.5 64.0 + - + +
139C SER* 3.3 19.9 + - - -
142C ARG* 5.6 0.4 - - - +
214C TRP* 5.1 19.1 - - + -
217C GLU* 3.2 16.5 + - - -
287C LEU* 5.1 15.8 - - - +
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Residues in contact with ALA 136 (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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91C THR* 6.1 0.2 - - + -
106C LEU* 4.7 6.5 - - + -
109C ILE* 4.4 15.0 - - + -
128C GLU* 3.6 35.7 - - + +
133C PRO* 5.1 0.2 - - + -
134C VAL 2.9 12.7 - - - +
135C ARG* 1.3 76.4 - - - +
137C ALA* 1.3 67.8 + - - +
139C SER* 3.1 10.1 + - - -
140C ILE* 3.0 26.3 + - - +
217C GLU* 3.5 4.0 + - - +
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Residues in contact with ALA 137 (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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128C GLU* 4.9 3.1 - - - +
135C ARG 3.4 0.2 - - - -
136C ALA* 1.3 78.7 - - - +
138C GLU* 1.3 64.7 + - - +
140C ILE* 3.3 7.0 + - - +
141C ARG* 2.9 29.2 + - - +
156C VAL* 4.0 14.2 - - + +
157C LEU 5.5 0.4 - - - +
158C SER* 4.7 6.7 - - - -
213C THR* 3.9 30.3 - - + +
217C GLU* 3.1 23.2 + - - +
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Residues in contact with GLU 138 (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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323A PHE* 3.3 13.9 - - + -
135C ARG* 2.5 54.8 + - + +
136C ALA 3.2 0.4 - - - -
137C ALA* 1.3 81.8 - - - +
139C SER* 1.3 55.9 + - - +
141C ARG* 3.5 24.4 + - - +
142C ARG* 2.9 51.9 + - - +
214C TRP* 5.8 2.3 - - - -
217C GLU* 4.9 0.4 + - - +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PHE* 3.6 37.1 - - - -
106C LEU* 3.8 16.4 - - - +
109C ILE* 4.0 12.3 - - - +
110C GLU* 4.7 12.4 - - - +
135C ARG 3.3 7.6 + - - -
136C ALA* 3.1 12.4 + - - -
138C GLU* 1.3 75.5 - - - +
140C ILE* 1.3 69.8 + - - +
142C ARG* 3.5 2.9 + - - +
143C ILE* 3.5 26.1 + - - +
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Residues in contact with ILE 140 (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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87C ILE* 3.8 23.3 - - + -
109C ILE* 3.7 19.1 - - + -
110C GLU* 6.4 0.2 - - - +
113C ALA* 4.2 13.2 - - + -
126C VAL* 4.4 7.4 - - + -
128C GLU* 3.8 29.4 - - + -
136C ALA 3.0 15.2 + - - +
137C ALA* 3.6 7.2 - - - +
139C SER* 1.3 79.5 + - - +
141C ARG* 1.3 65.9 + - - +
143C ILE* 3.0 14.7 + - - +
144C PHE* 3.1 46.3 + - + -
156C VAL* 4.1 13.5 - - + -
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Residues in contact with ARG 141 (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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137C ALA* 2.9 22.9 + - - +
138C GLU* 3.5 31.1 + - - +
139C SER 3.4 0.2 - - - -
140C ILE* 1.3 77.9 - - - +
142C ARG* 1.3 57.1 + - - +
144C PHE* 3.3 3.7 + - + +
145C ASP* 2.9 49.5 + - - +
156C VAL* 3.8 27.7 - - + +
183C ASP* 4.1 23.8 + - - -
213C THR* 2.9 35.6 + - - +
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Residues in contact with ARG 142 (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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320A ASP 4.5 1.4 + - - -
321A SER* 3.6 24.2 + - - +
323A PHE* 2.8 37.9 - - + -
435A PRO* 4.0 15.0 - - + +
437A PHE* 4.7 8.6 - - - -
458A GLN* 4.6 15.3 - - - +
135C ARG* 5.6 0.6 - - - +
138C GLU* 2.9 46.5 + - - +
139C SER 3.5 4.5 + - - +
140C ILE 3.2 0.8 + - - -
141C ARG* 1.3 75.8 - - - +
143C ILE* 1.3 61.3 + - + +
145C ASP* 4.0 9.4 - - + +
146C ALA* 3.4 21.7 + - - +
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Residues in contact with ILE 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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435A PRO* 5.1 6.3 - - + -
110C GLU* 3.7 55.6 - - + +
113C ALA* 3.9 19.7 - - + +
114C ARG* 3.9 40.6 - - + +
117C VAL* 4.8 2.7 - - + -
139C SER 3.5 9.8 + - - +
140C ILE 3.0 8.1 + - - +
142C ARG* 1.3 79.1 - - + +
144C PHE* 1.3 60.4 + - + +
146C ALA 3.4 1.6 + - - -
147C ASN* 3.1 46.0 + - - +
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Residues in contact with PHE 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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113C ALA* 3.3 36.1 - - + -
116C ILE* 3.9 13.0 - - + -
117C VAL* 3.6 21.1 - - + -
126C VAL* 3.5 37.5 - - + -
140C ILE* 3.1 27.0 + - + -
141C ARG* 3.8 6.7 - - + +
143C ILE* 1.3 78.9 - - + +
145C ASP* 1.3 66.0 + - - +
146C ALA 3.3 0.7 + - - -
147C ASN 3.5 16.5 - - - +
148C THR* 4.0 4.9 + - - -
152C LEU* 5.9 0.5 - - - +
154C LEU* 3.6 29.7 - - + +
156C VAL* 3.9 19.1 - - + -
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Residues in contact with ASP 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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141C ARG* 2.9 38.2 + - - +
142C ARG* 4.0 11.7 - - + +
143C ILE 3.4 0.2 - - - -
144C PHE* 1.3 77.6 - - - +
146C ALA* 1.3 60.4 + - - +
148C THR* 4.2 14.7 - - - +
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Residues in contact with ALA 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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434A LYS* 3.3 18.7 - - + +
435A PRO* 3.1 54.7 - - + -
142C ARG* 3.4 5.7 + - + +
143C ILE 3.4 2.5 + - - +
144C PHE 3.2 0.4 - - - -
145C ASP* 1.3 78.8 - - - +
147C ASN* 1.3 59.0 + - - +
148C THR* 3.3 10.6 + - - +
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Residues in contact with ASN 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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433A LEU* 4.8 7.6 - - - +
434A LYS* 2.7 45.8 + - - +
114C ARG* 4.0 11.9 - - - +
117C VAL* 3.7 38.1 - - + +
143C ILE* 3.1 31.9 + - - +
144C PHE 3.5 9.6 - - - +
146C ALA* 1.3 74.0 - - - +
148C THR* 1.3 58.5 + - - +
149C LYS* 3.8 2.5 + - - -
152C LEU* 4.2 5.7 - - - +
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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