Contacts of the helix formed by residues 129 - 143 (chain C) in PDB entry 1RJF
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 TYR 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C ASP* 1.3 91.3 + - - +
130C ASN* 1.3 66.2 - - - +
131C GLU* 3.2 10.5 - - + +
132C SER* 3.2 20.7 + - - +
133C VAL* 3.2 10.2 + - - +
174C CYS 4.0 12.3 - - - -
175C ASP* 3.5 28.0 + - + -
176C LEU* 4.6 7.0 - - + -
177C ASN* 3.7 17.0 + - - -
203C LEU* 6.5 0.7 - - + -
207C MET* 6.1 0.7 - - - +
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Residues in contact with ASN 130 (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 ASP 3.8 0.2 + - - -
129C TYR* 1.3 73.2 - - - +
131C GLU* 1.3 76.8 + - - +
133C VAL* 3.7 0.9 - - - +
134C GLU* 3.2 47.5 + - - +
163C LEU* 5.5 1.4 - - - +
173C ALA* 3.5 29.5 - - + +
174C CYS 4.9 1.4 - - - +
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C TYR* 3.2 6.7 - - + +
130C ASN* 1.3 95.2 + - - +
132C SER* 1.3 64.7 + - - +
134C GLU* 3.7 4.8 + - - +
135C LEU* 3.5 21.5 + - - +
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Residues in contact with SER 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 5.3 9.4 - - - +
107C GLY* 5.0 8.1 - - - +
128C ASP* 3.4 31.3 + - - -
129C TYR* 3.2 18.3 + - - +
131C GLU* 1.3 79.9 - - - +
133C VAL* 1.3 56.8 + - - +
135C LEU* 3.7 4.5 + - - +
136C LYS* 3.3 25.3 + - - +
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Residues in contact with VAL 133 (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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106C CYS* 5.1 1.8 - - - -
128C ASP* 3.6 29.2 - - + +
129C TYR 3.2 11.2 + - - +
130C ASN 3.7 6.3 - - - +
132C SER* 1.3 74.5 - - - +
134C GLU* 1.3 63.2 + - - +
136C LYS* 3.9 7.9 - - + -
137C ASN* 3.1 27.4 + - - +
163C LEU* 3.4 20.4 - - + +
171C LEU* 3.4 27.2 - - + +
172C ALA 3.5 16.8 - - - +
173C ALA* 3.7 22.9 - - + +
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASN* 3.2 36.9 + - - +
131C GLU* 4.0 6.1 - - - +
132C SER 3.3 0.4 - - - -
133C VAL* 1.3 77.4 - - - +
135C LEU* 1.3 60.9 + - - +
137C ASN* 3.6 5.5 + - - +
138C SER* 3.0 27.4 + - - -
156C ASP* 5.0 3.1 - - - +
163C LEU* 3.6 33.7 - - + +
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Residues in contact with LEU 135 (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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10C TYR* 3.7 29.4 - - + +
48C TYR* 5.8 0.4 - - - +
52C LEU* 4.0 18.2 - - + -
55C PHE* 4.1 27.4 - - + +
56C SER* 5.3 3.8 - - - -
59C ALA* 5.1 1.1 - - + -
131C GLU 3.5 14.6 + - - +
132C SER* 4.0 4.7 - - - +
133C VAL 3.4 0.2 - - - -
134C GLU* 1.3 76.9 - - - +
136C LYS* 1.3 64.5 + - - +
138C SER* 3.4 4.9 + - - -
139C ILE* 3.2 40.3 + - + +
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Residues in contact with LYS 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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48C TYR* 3.9 21.3 - - + +
106C CYS* 4.1 3.5 - - - -
107C GLY 3.2 25.7 + - - +
108C SER* 4.7 0.7 - - - +
109C ASP* 2.8 31.3 + - - +
110C LEU* 4.5 8.3 - - - -
112C MET* 3.8 13.7 - - - -
126C ASP* 2.9 29.2 + - - -
132C SER 3.3 16.8 + - - +
133C VAL* 4.1 7.2 - - - +
134C GLU 3.4 0.2 - - - -
135C LEU* 1.3 76.5 - - - +
137C ASN* 1.3 63.2 + - - +
139C ILE* 4.1 1.2 - - - +
140C LEU* 3.2 35.6 + - + +
169C TYR* 3.9 3.4 - - - -
171C LEU* 4.2 15.5 - - + -
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Residues in contact with ASN 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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133C VAL 3.1 20.2 + - - +
134C GLU* 3.7 8.9 + - - +
135C LEU 3.3 0.4 - - - -
136C LYS* 1.3 75.8 - - - +
138C SER* 1.3 65.2 + - - +
140C LEU* 4.4 0.5 - - - +
141C ARG* 3.2 38.8 + - - +
156C ASP* 3.5 31.3 + - - -
163C LEU* 3.3 28.2 + - + +
164C ILE* 3.1 29.2 - - - +
171C LEU* 4.0 9.6 - - + +
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Residues in contact with SER 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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55C PHE* 3.2 35.6 - - - -
134C GLU* 3.0 15.6 + - - -
135C LEU* 3.7 11.8 - - - -
136C LYS 3.3 0.6 - - - -
137C ASN* 1.3 81.0 + - - +
139C ILE* 1.3 57.1 + - - +
140C LEU 3.5 0.2 - - - -
141C ARG* 3.7 3.3 + - - +
142C GLU* 3.1 31.4 + - - +
156C ASP* 6.1 0.7 - - - -
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Residues in contact with ILE 139 (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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48C TYR* 3.4 56.3 - - + +
51C THR* 3.7 31.7 - - + +
52C LEU* 3.9 20.0 - - + -
55C PHE* 4.3 10.1 - - + -
135C LEU* 3.2 38.2 + - + +
136C LYS 3.5 4.2 + - - +
137C ASN 3.4 0.2 - - - -
138C SER* 1.3 76.1 - - - +
140C LEU* 1.3 63.2 + - - +
143C SER* 3.3 24.1 + - - -
146C LEU* 4.0 4.6 - - + +
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Residues in contact with LEU 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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48C TYR* 4.9 2.9 - - + -
110C LEU* 4.4 20.0 - - + -
112C MET* 4.3 3.6 - - + -
113C LEU* 5.2 0.7 - - + -
136C LYS* 3.2 32.7 + - + +
137C ASN 4.4 2.2 - - - +
139C ILE* 1.3 76.6 - - - +
141C ARG* 1.3 60.4 + - - +
142C GLU 3.7 0.2 + - - -
143C SER 3.8 1.9 - - - +
146C LEU* 3.8 26.8 - - + -
147C ARG* 3.5 29.5 + - - +
150C LEU* 4.0 21.5 - - + -
152C LEU* 4.4 13.4 - - + +
164C ILE* 3.8 19.3 - - + -
169C TYR* 3.7 23.1 - - - +
171C LEU* 4.9 0.2 - - + -
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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 ASN* 3.2 36.0 + - - +
138C SER* 4.3 3.4 - - - +
139C ILE 3.3 0.2 - - - -
140C LEU* 1.3 78.0 - - + +
142C GLU* 1.3 59.0 + - - +
147C ARG* 3.3 24.7 + - - +
152C LEU* 3.9 19.7 - - + +
153C SER* 3.4 32.9 + - - +
154C LYS* 3.4 21.0 - - - +
155C GLU* 3.4 29.9 + - - +
156C ASP* 4.0 13.5 - - - +
157C THR* 4.2 10.9 + - - +
158C ALA* 4.3 9.1 - - - +
163C LEU 3.4 19.4 + - - -
164C ILE* 3.8 20.4 - - + +
165C ASP 4.9 1.4 - - - +
166C GLN* 5.4 2.6 + - - -
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Residues in contact with GLU 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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51C THR* 3.7 17.3 - - + -
54C LYS* 3.8 34.6 + - + +
55C PHE* 3.5 20.8 - - + -
138C SER 3.1 20.2 + - - +
140C LEU 3.4 0.2 - - - -
141C ARG* 1.3 77.4 - - - +
143C SER* 1.3 67.4 + - - +
144C GLU* 3.5 1.2 + - - +
147C ARG* 3.2 10.6 + - - -
154C LYS* 5.6 2.9 - - - +
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Residues in contact with SER 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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47C SER* 2.7 24.3 + - - -
51C THR* 3.4 20.8 - - - +
139C ILE 3.3 14.5 + - - -
140C LEU 3.8 0.9 - - - +
142C GLU* 1.3 82.0 - - - +
144C GLU* 1.3 65.0 + - - +
145C ILE* 3.6 2.8 - - - +
146C LEU* 3.6 25.6 + - - +
147C ARG* 3.2 24.3 + - - +
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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