Contacts of the helix formed by residues 130 - 143 (chain Y) in PDB entry 6CP3
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 ASP 130 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129Y LEU* 1.3 82.0 - - - +
131Y PRO* 1.3 74.3 - - + +
132Y LYS* 3.5 9.4 - - + +
133Y SER* 3.2 10.2 + - - +
134Y PHE* 3.0 19.1 - - - -
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Residues in contact with PRO 131 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Y ASP* 1.3 91.8 - - + +
132Y LYS* 1.3 61.6 + - + +
133Y SER 3.3 0.9 - - - -
134Y PHE* 3.0 10.6 + - + +
135Y LYS* 2.8 50.4 + - + +
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Residues in contact with LYS 132 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Y ASP* 3.5 5.5 - - + +
131Y PRO* 1.3 84.3 - - + +
133Y SER* 1.3 64.0 + - - +
135Y LYS* 3.3 6.8 + - + +
136Y ARG* 2.9 44.7 + - + +
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Residues in contact with SER 133 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Y LEU* 3.6 18.2 - - - +
130Y ASP* 3.2 19.8 + - - +
132Y LYS* 1.3 75.2 - - - +
134Y PHE* 1.3 73.2 + - - -
136Y ARG* 3.3 11.1 + - - +
137Y ILE* 3.0 33.1 + - - +
167Y LEU* 6.0 4.3 - - - -
193Z VAL* 5.6 7.2 - - - -
197Z SER* 4.7 13.9 - - - -
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Residues in contact with PHE 134 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Y VAL* 6.1 4.0 - - + -
128Y PRO* 5.5 1.8 - - + -
129Y LEU* 3.7 19.7 - - + -
130Y ASP 3.0 22.0 - - - -
131Y PRO* 3.0 13.1 + - + +
133Y SER* 1.3 87.2 + - - +
135Y LYS* 1.3 59.4 + - + +
137Y ILE* 3.3 3.8 + - - +
138Y GLU* 2.9 50.1 + - - +
155Y LEU 5.6 4.5 - - - -
157Y ASN* 3.1 53.4 - - + -
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Residues in contact with LYS 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Y PRO* 2.8 37.9 + - - +
132Y LYS* 3.8 6.5 - - - +
134Y PHE* 1.3 74.5 - - + +
136Y ARG* 1.3 57.4 + - - +
138Y GLU* 3.3 18.0 + - - +
139Y LYS* 2.9 38.0 + - + +
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Residues in contact with ARG 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132Y LYS* 2.9 37.4 + - + +
133Y SER* 4.0 10.3 - - - +
135Y LYS* 1.3 78.0 - - - +
137Y ILE* 1.3 68.2 + - + +
139Y LYS* 3.6 8.1 + - - +
140Y ALA* 3.0 26.9 + - - +
194Z LEU* 6.5 0.7 - - - -
197Z SER* 4.5 17.0 - - - -
198Z ILE* 6.5 0.2 - - - -
201Z ILE* 3.7 31.3 - - + +
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Residues in contact with ILE 137 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Y VAL* 4.1 28.9 - - + -
133Y SER* 3.0 23.6 + - - +
134Y PHE* 3.8 4.0 - - - +
136Y ARG* 1.3 87.0 - - + +
138Y GLU* 1.3 65.1 + - + +
140Y ALA* 3.1 4.9 + - + +
141Y LEU* 2.9 50.8 + - + +
167Y LEU* 5.9 3.6 - - + -
169Y VAL* 5.7 1.1 - - + -
197Z SER* 4.3 23.1 - - - +
200Z GLU* 2.9 37.5 - - + +
201Z ILE* 5.3 3.1 - - + -
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Residues in contact with GLU 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Y PHE* 2.9 50.7 + - - +
135Y LYS* 3.3 23.5 + - - +
137Y ILE* 1.3 76.2 - - + +
139Y LYS* 1.3 63.0 + - + +
141Y LEU* 3.3 6.8 + - - +
142Y SER* 2.9 29.8 + - - +
153Y LEU* 5.5 6.1 - - - +
155Y LEU* 3.9 32.4 - - + +
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Residues in contact with LYS 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Y LYS* 2.9 25.0 + - + +
136Y ARG* 3.6 8.3 - - - +
138Y GLU* 1.3 76.5 - - + +
140Y ALA* 1.3 52.9 + - - +
142Y SER* 3.0 8.9 + - - -
143Y ALA* 2.4 41.9 + - + +
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Residues in contact with ALA 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Y ARG 3.0 19.1 + - - +
137Y ILE* 3.1 9.8 + - + +
139Y LYS* 1.3 74.6 - - - +
141Y LEU* 1.3 55.8 + - + +
143Y ALA* 2.5 40.8 - - - +
144Y SER* 3.3 3.8 + - - -
200Z GLU* 5.1 2.0 - - + +
201Z ILE* 4.9 15.0 - - + +
204Z LEU* 3.6 14.2 - - + +
205Z LEU* 4.4 18.3 - - + +
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Residues in contact with LEU 141 (chain Y).
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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121Y GLY* 5.4 3.4 - - - -
122Y THR 5.7 1.6 - - - +
123Y VAL* 5.5 4.9 - - + -
137Y ILE* 2.9 48.8 + - + +
138Y GLU* 3.6 5.6 - - - +
140Y ALA* 1.3 73.6 - - + +
142Y SER* 1.3 59.8 + - - +
144Y SER* 2.5 21.1 + - - -
146Y LEU* 4.8 0.9 - - + +
147Y VAL* 3.5 16.0 - - + +
153Y LEU* 5.3 7.6 - - + -
154Y LYS 5.3 4.0 - - - +
155Y LEU* 5.2 13.9 - - + -
169Y VAL* 5.1 14.4 - - + -
170Y GLU 5.3 1.6 - - - +
171Y LEU* 3.4 33.6 - - + +
200Z GLU* 5.6 3.4 - - + +
204Z LEU* 3.3 24.7 - - + -
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Residues in contact with SER 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Y GLU* 2.9 16.6 + - - +
139Y LYS* 3.3 11.9 - - - -
141Y LEU* 1.3 75.9 - - - +
143Y ALA* 1.3 57.7 + - - +
144Y SER 3.1 11.3 + - - +
147Y VAL* 4.7 14.4 - - - +
149Y GLN* 5.7 4.3 - - - +
153Y LEU* 3.9 17.8 + - - +
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Residues in contact with ALA 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139Y LYS* 2.4 28.5 + - + +
140Y ALA* 2.5 17.5 - - - +
142Y SER* 1.3 68.6 - - - +
144Y SER* 1.3 55.5 + - - +
204Z LEU 4.3 3.3 - - - +
205Z LEU* 4.0 26.9 - - + +
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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