Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 5V5Z
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 PRO 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU* 4.1 6.7 - - - +
134A CYS* 1.3 92.6 - - + +
136A ASN* 1.3 66.6 + - - +
137A SER* 3.2 9.4 - - - +
138A ARG* 3.0 34.7 + - + +
139A LEU* 3.1 9.8 + - - +
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Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.1 21.9 - - + +
115A GLU* 4.1 16.4 + - - +
134A CYS 3.9 0.4 + - - -
135A PRO* 1.3 72.9 - - - +
137A SER* 1.3 59.1 + - - +
139A LEU* 3.0 11.1 + - - +
140A MET* 2.8 59.2 + - - +
467A ARG* 3.3 30.8 - - - +
468A HIS* 3.6 18.4 + - - -
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PRO* 3.2 8.0 - - - +
136A ASN* 1.3 82.5 - - - +
138A ARG* 1.3 76.4 + - - +
140A MET* 3.4 10.9 + - - +
141A GLU* 3.3 23.1 + - - +
287A LYS* 5.3 8.1 - - - +
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Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A CYS* 3.6 17.5 - - + -
135A PRO* 3.0 35.2 + - + +
137A SER* 1.3 85.9 + - - +
139A LEU* 1.3 66.4 + - - +
141A GLU* 3.1 19.7 + - - +
142A GLN* 3.2 21.6 + - - +
286A TYR* 2.9 48.0 - - - +
288A ASP* 2.8 42.0 + - - -
290A VAL* 4.2 12.0 - - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 5.7 2.0 - - - +
131A ILE* 3.7 39.3 - - + +
132A TYR* 4.0 9.0 - - + -
134A CYS* 4.0 1.9 - - - +
135A PRO 3.1 10.2 + - - +
136A ASN* 3.0 12.5 + - - +
138A ARG* 1.3 75.5 - - - +
140A MET* 1.3 76.2 + - + +
142A GLN* 3.2 14.4 + - + +
143A LYS* 3.1 46.0 + - + +
468A HIS* 4.0 16.4 - - + +
601A HEM 3.6 31.6 - - + +
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN* 2.8 54.2 + - - +
137A SER* 3.6 9.2 - - - +
138A ARG 3.2 0.4 - - - -
139A LEU* 1.3 93.9 - - + +
141A GLU* 1.3 57.7 + - + +
143A LYS* 3.4 7.9 + - + +
144A LYS* 3.1 20.4 + - - +
287A LYS* 6.1 2.9 - - - -
447A TYR* 4.1 22.0 - - - +
448A GLY* 4.2 14.1 - - - -
449A PHE* 3.6 35.6 - - + +
467A ARG* 3.4 26.5 - - + +
468A HIS* 4.6 1.1 - - - +
601A HEM 4.5 0.9 - - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A SER* 3.3 20.0 + - - +
138A ARG* 3.1 8.2 + - - +
140A MET* 1.3 71.4 - - + +
142A GLN* 1.3 56.9 + - - +
143A LYS 3.1 1.8 - - - -
144A LYS* 2.9 13.6 + - + +
145A PHE* 2.6 61.4 + - + -
285A THR 4.8 0.5 - - - +
286A TYR* 3.6 19.1 - - + +
287A LYS* 3.1 60.9 + - - +
448A GLY 5.4 0.4 - - - -
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY 3.7 1.8 + - - -
130A VAL* 3.4 21.9 - - - +
131A ILE* 3.0 23.6 + - - -
134A CYS* 3.1 31.9 - - - -
138A ARG* 3.2 14.5 + - - +
139A LEU* 3.2 10.7 + - + +
141A GLU* 1.3 73.9 - - - +
143A LYS* 1.4 58.4 + - + +
145A PHE* 3.4 12.1 + - - +
146A ALA* 3.0 28.6 + - - +
286A TYR* 3.6 23.3 + - + +
292A MET* 4.5 5.8 - - - -
300A LEU* 3.6 27.5 - - + +
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 3.1 30.0 + - + +
140A MET* 3.6 9.0 - - + +
142A GLN* 1.4 73.7 - - + +
144A LYS* 1.3 64.5 + - - +
146A ALA* 3.7 3.1 - - - +
147A LYS* 3.2 27.9 + - - +
449A PHE* 3.3 24.1 - - + -
467A ARG 2.9 20.5 + - - +
468A HIS 3.4 1.2 - - - -
469A ARG 2.6 29.5 + - - -
471A ILE* 3.5 29.4 - - + +
601A HEM 2.8 42.8 + - + +
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET 3.1 8.5 + - - +
141A GLU* 2.9 17.1 + - - +
143A LYS* 1.3 74.2 - - - +
145A PHE* 1.3 73.0 + - + +
147A LYS* 2.9 17.9 + - + +
148A PHE* 3.2 34.1 - - + -
446A ASP* 5.6 1.6 + - - -
448A GLY 3.6 26.1 + - - +
449A PHE* 3.5 10.1 - - - +
450A GLY* 4.6 10.7 - - - +
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 2.6 47.1 + - + +
142A GLN* 3.5 12.1 - - - +
144A LYS* 1.3 77.7 - - + +
146A ALA* 1.3 64.7 + - - +
148A PHE* 3.2 29.5 + + - +
149A ALA 4.6 0.3 + - - -
279A SER* 4.5 8.5 - - - +
280A LEU* 4.0 14.1 + - + -
283A HIS* 3.4 34.5 - - + +
284A SER* 3.9 18.8 - - - -
285A THR 3.8 20.0 - - - -
286A TYR* 3.6 32.8 - + - -
292A MET* 3.9 13.0 - - - -
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLN 3.0 18.0 + - - +
143A LYS* 3.7 7.2 - - - +
145A PHE* 1.3 77.6 - - - +
147A LYS* 1.3 57.6 + - - +
148A PHE 2.8 7.6 + - - -
149A ALA* 3.1 11.6 + - - +
150A LEU* 3.6 13.3 - - + +
276A LEU* 3.8 26.2 - - + +
280A LEU* 4.8 2.6 - - + +
300A LEU* 5.8 0.2 - - + -
304A ILE* 4.6 15.3 - - + -
471A ILE* 4.2 17.9 - - + -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS 3.2 13.9 + - - +
144A LYS* 2.9 13.3 + - + +
146A ALA* 1.3 76.9 - - - +
148A PHE* 1.3 58.2 + - + +
149A ALA 3.2 0.7 - - - -
150A LEU* 3.1 35.7 + - + +
151A THR* 3.6 11.1 - - - +
449A PHE* 2.9 31.9 + - + +
450A GLY* 4.3 11.7 - - - -
451A LYS 5.0 5.1 + - - +
452A VAL* 6.1 1.2 - - - +
471A ILE* 4.0 32.3 - - + +
474A GLN* 5.6 11.4 + - - +
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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