Contacts of the helix formed by residues 138 - 145 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F THR* 3.3 10.5 - - - +
137F GLY* 1.3 80.0 - - - +
139F LYS* 1.3 67.6 + - - +
140F VAL* 3.8 22.4 - - + -
141F VAL* 4.2 11.0 - - + -
142F ASP* 3.0 25.9 + - - +
166F PHE* 3.6 31.6 - - + -
169F GLU* 4.0 25.1 - - + +
170F LEU* 3.8 24.7 - - + -
173F ASN* 4.6 1.6 - - - +
346F PRO* 4.9 0.7 - - + -
416F GLN* 3.3 13.7 - - - +
418F PHE* 4.1 15.5 - - + -
432F VAL 4.9 1.6 - - - +
437F THR* 5.5 0.3 + - - -
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Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ILE* 1.3 71.2 - - - +
140F VAL* 1.3 60.2 + - + +
141F VAL 3.2 0.2 + - - -
142F ASP 3.2 1.2 + - - -
143F LEU* 2.9 36.0 + - - +
413F PHE* 2.3 62.5 + - - -
414F LEU* 4.6 7.0 - - - +
415F SER 3.8 17.1 + - - +
416F GLN* 2.6 28.8 + - + +
432F VAL* 4.5 12.8 - - + -
437F THR* 4.3 20.9 - - + +
441F PHE* 4.3 11.4 - - + -
460F VAL* 4.0 2.0 - - - +
461F GLY* 3.2 28.3 + - - +
462F GLY* 5.6 0.2 - - - -
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Residues in contact with VAL 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F ILE* 3.8 16.8 - - + -
139F LYS* 1.3 72.0 - - - +
141F VAL* 1.3 67.3 + - + +
143F LEU* 5.0 2.2 - - - -
144F LEU* 3.6 24.2 + - + +
145F ALA* 4.1 2.4 + - - +
166F PHE* 5.2 0.2 - - + -
346F PRO* 4.0 15.0 - - + +
348F VAL* 3.7 44.2 - - + +
353F SER* 6.0 0.5 - - - -
414F LEU* 3.3 57.0 - - + +
416F GLN* 5.4 0.4 - - - +
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F THR* 3.8 9.6 - - - +
138F ILE* 3.9 13.1 + - + -
139F LYS 3.2 0.6 - - - -
140F VAL* 1.3 79.4 - - + +
142F ASP* 1.3 72.7 + - - +
143F LEU 3.1 1.7 + - - -
145F ALA* 2.9 52.7 + - - +
147F TYR* 3.5 51.1 - - + +
166F PHE* 3.6 22.7 - - + -
333F THR* 5.2 5.2 - - + +
348F VAL* 5.6 0.4 - - + -
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Residues in contact with ASP 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LEU 3.9 5.2 - - - +
135F GLU* 4.2 7.2 - - - +
136F THR* 2.8 30.3 + - - +
137F GLY* 2.5 34.1 + - - -
138F ILE 3.0 13.4 + - - +
139F LYS* 3.2 2.9 + - - +
141F VAL* 1.3 81.9 - - - +
143F LEU* 1.3 56.9 + - - +
146F PRO* 4.7 9.8 - - - +
147F TYR 5.0 2.1 + - - -
367F HIS* 3.0 22.9 + - - -
432F VAL 4.9 0.5 - - - +
433F ARG 6.1 0.2 - - - -
434F LEU* 4.3 29.1 - - + +
437F THR* 5.8 5.4 - - - +
438F VAL* 5.4 0.7 - - - +
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Residues in contact with LEU 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LYS 2.9 17.3 + - - +
140F VAL* 4.8 0.7 - - - +
142F ASP* 1.3 79.6 - - - +
144F LEU* 1.3 85.1 + - + +
145F ALA 3.6 0.4 - - - -
146F PRO* 5.3 0.2 - - - -
358F LEU* 3.6 6.1 - - - +
367F HIS* 3.2 30.0 - - + +
370F VAL* 3.9 25.8 - - + -
371F ALA* 3.9 8.2 - - - +
374F VAL* 4.3 10.3 - - + -
414F LEU* 5.0 1.1 - - + -
437F THR* 4.6 8.7 - - + +
438F VAL* 5.0 8.3 - - + -
441F PHE* 3.6 50.9 - - + -
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 3.6 16.1 + - + +
141F VAL 3.3 1.4 + - - -
143F LEU* 1.3 103.1 - - + +
145F ALA* 1.3 61.9 + - + +
348F VAL* 6.1 1.6 - - + -
350F PRO* 3.8 38.1 - - + +
353F SER* 4.7 9.5 - - - +
354F LYS* 5.4 1.0 - - - -
355F SER* 5.3 0.3 + - - -
358F LEU* 3.3 17.9 - - - +
371F ALA* 4.1 16.6 - - + +
374F VAL* 4.1 15.0 - - + -
375F GLN* 4.0 38.0 + - + +
414F LEU* 4.7 12.3 - - + -
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Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL 4.1 2.9 + - - +
141F VAL* 2.9 25.3 + - - +
144F LEU* 1.3 82.5 - - + +
146F PRO* 1.3 70.8 - - - +
147F TYR* 3.4 8.6 + - + -
332F THR 4.3 5.8 - - - +
333F THR* 5.0 3.8 - - - +
353F SER* 4.1 17.7 - - - -
354F LYS 3.5 26.9 - - - +
355F SER* 4.3 4.7 - - - -
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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