Contacts of the helix formed by residues 138 - 144 (chain D) 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 ILE 138 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 3.1 8.0 + - - +
137D GLY* 1.3 84.4 - - - +
139D LYS* 1.3 67.2 + - - +
140D VAL* 3.4 25.6 - - + +
141D VAL* 4.2 9.2 - - + +
142D ASP* 3.0 26.2 + - - +
166D PHE* 3.7 30.1 - - + -
169D GLU* 4.7 7.2 - - + -
170D LEU* 4.3 22.4 - - + -
173D ASN* 4.6 8.7 - - - +
346D PRO* 5.2 0.7 - - + -
416D GLN* 3.4 16.2 - - - +
418D PHE* 4.1 26.2 - - + -
432D VAL 4.8 1.7 - - - +
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Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLY 4.2 0.2 + - - -
138D ILE* 1.3 74.0 - - - +
140D VAL* 1.3 60.3 + - - +
142D ASP* 3.1 2.6 + - - -
143D LEU* 2.9 34.0 + - - +
413D PHE* 3.3 42.2 - - + -
414D LEU* 4.5 7.4 - - + +
415D SER 3.5 4.9 + - - -
416D GLN* 3.0 44.8 + - - +
432D VAL* 3.8 27.8 - - + +
437D THR* 3.8 25.5 - - + +
441D PHE* 4.9 3.8 - - + -
460D VAL 3.6 11.2 + - - -
461D GLY* 4.2 15.3 - - - +
462D GLY* 5.2 0.4 - - - -
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ILE* 3.7 16.8 - - + +
139D LYS* 1.3 75.7 - - - +
141D VAL* 1.3 69.9 + - + +
143D LEU* 4.2 1.8 - - - -
144D LEU* 3.7 26.1 + - + +
145D ALA* 4.3 0.9 + - - +
166D PHE* 5.1 0.7 - - + -
346D PRO* 4.5 11.0 - - + +
348D VAL* 3.7 48.6 - - + +
350D PRO* 5.4 0.2 - - + -
414D LEU* 3.7 51.6 + - + +
416D GLN* 4.9 0.6 + - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 4.3 7.0 - - + +
138D ILE* 3.8 15.6 + - + +
139D LYS 3.2 0.4 - - - -
140D VAL* 1.3 80.4 - - + +
142D ASP* 1.3 74.3 + - - +
143D LEU 3.2 0.2 + - - -
145D ALA* 2.9 48.3 + - - +
147D TYR* 3.4 51.4 - - + +
166D PHE* 3.7 22.9 - - + -
333D THR* 4.5 8.5 - - + +
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Residues in contact with ASP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 5.4 3.3 - - + +
134D LEU 3.4 19.6 - - - +
135D GLU* 3.9 13.4 - - - +
136D THR* 3.2 27.1 + - - -
137D GLY* 3.3 7.1 + - - -
138D ILE 3.0 19.1 + - - +
139D LYS* 3.1 5.1 + - - +
141D VAL* 1.3 81.1 - - - +
143D LEU* 1.3 57.8 + - - +
146D PRO* 4.7 12.8 - - - +
367D HIS* 3.0 21.5 + - - -
432D VAL 5.0 2.3 - - - +
434D LEU* 3.4 27.8 - - + +
437D THR* 5.8 2.2 - - + +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LYS 2.9 16.2 + - - +
140D VAL* 4.6 2.0 - - - +
141D VAL 3.2 0.2 + - - -
142D ASP* 1.3 77.7 - - - +
144D LEU* 1.3 82.2 + - + +
146D PRO* 5.2 0.2 - - - -
367D HIS* 3.2 33.4 - - + +
370D VAL* 4.0 22.0 - - + -
371D ALA* 4.1 13.7 - - + +
374D VAL* 4.1 17.7 - - + -
414D LEU* 4.9 2.5 - - + -
434D LEU* 5.4 0.4 - - - -
437D THR* 4.9 3.6 - - + +
438D VAL* 5.2 6.1 - - + -
441D PHE* 3.6 54.7 - - + -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 3.7 24.3 + - + +
141D VAL 3.5 1.2 + - - -
143D LEU* 1.3 97.8 - - + +
145D ALA* 1.3 60.4 + - + +
146D PRO* 3.3 10.9 - - - +
348D VAL* 5.4 1.6 - - + -
350D PRO* 3.5 46.0 - - + +
353D SER* 4.5 13.2 - - - +
354D LYS* 5.8 0.3 - - - -
355D SER* 5.1 0.9 + - - -
358D LEU* 3.3 28.8 - - + +
371D ALA* 4.6 15.3 - - + +
374D VAL* 4.4 13.7 - - + -
375D GLN* 5.3 10.5 - - + +
414D LEU* 4.7 5.6 - - + -
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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