Contacts of the helix formed by residues 320 - 328 (chain M) in PDB entry 1L0V
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 GLY 320 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319M LEU* 1.3 82.5 - - - +
321M GLU* 1.3 78.6 + - - +
322M LYS 3.8 1.1 - - - -
323M LYS* 4.5 7.2 - - - +
324M LEU* 3.2 17.1 + - - +
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Residues in contact with GLU 321 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319M LEU 4.2 0.3 - - - +
320M GLY* 1.3 89.8 - - - +
322M LYS* 1.3 54.3 + - - +
323M LYS 2.4 18.8 + - - -
324M LEU* 4.0 3.5 - - - +
325M HIS* 3.0 51.8 + - + +
326M GLU* 4.2 0.3 - - - +
344M VAL* 3.4 26.0 - - - +
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Residues in contact with LYS 322 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320M GLY 3.8 0.4 - - - -
321M GLU* 1.3 73.9 - - - +
323M LYS* 1.3 52.5 + - - +
326M GLU* 2.9 46.3 + - + +
327M ARG* 2.7 43.8 + - - +
101O GLU* 5.5 7.3 + - - -
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Residues in contact with LYS 323 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250M GLU* 3.9 24.2 - - + +
319M LEU* 4.2 31.4 - - + -
320M GLY 4.0 13.0 - - - +
321M GLU 2.4 6.8 + - - -
322M LYS* 1.3 77.6 - - - +
324M LEU* 1.3 60.0 + - - +
325M HIS 3.5 0.2 - - - -
326M GLU* 4.5 0.2 - - - +
327M ARG* 2.8 86.8 + - - +
328M LEU* 3.3 4.4 + - - +
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Residues in contact with LEU 324 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316M LEU* 3.9 16.8 - - + +
319M LEU* 3.6 37.9 - - + +
320M GLY 3.2 12.5 + - - +
321M GLU* 3.2 8.0 + - - +
323M LYS* 1.3 80.5 - - - +
325M HIS* 1.3 62.6 + - + +
326M GLU 3.4 0.2 - - - -
328M LEU* 3.3 42.3 + - + +
329M PRO* 3.7 0.7 - - - +
331M ILE* 6.1 0.2 - - + -
332M CYS* 3.1 32.9 - - - -
343M PRO* 3.0 35.4 - - + +
344M VAL* 3.4 9.4 - - + -
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Residues in contact with HIS 325 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321M GLU* 3.0 46.0 + - + +
324M LEU* 1.3 80.1 + - + +
326M GLU* 1.3 62.0 + - - +
329M PRO* 4.2 13.8 - - - +
332M CYS* 3.9 27.6 - - + +
342M ASP* 5.1 5.1 + - - -
344M VAL* 4.5 9.6 - - + +
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Residues in contact with GLU 326 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321M GLU 4.2 6.1 - - - +
322M LYS* 2.9 50.5 + - + +
324M LEU 3.4 0.8 + - - -
325M HIS* 1.3 78.9 - - - +
327M ARG* 1.3 76.3 + - + +
328M LEU 3.8 0.4 - - - -
329M PRO* 4.1 10.0 - - - +
101O GLU* 5.6 4.5 - - - +
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Residues in contact with ARG 327 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M ASP* 3.9 13.9 - - - +
250M GLU* 3.4 30.9 + - + +
322M LYS* 2.7 37.0 + - - +
323M LYS* 2.8 58.7 + - - +
326M GLU* 1.3 95.6 + - + +
328M LEU* 1.3 75.7 + - + +
329M PRO* 3.4 7.3 - - - +
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Residues in contact with LEU 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M ASP* 4.3 0.2 - - - -
244M THR* 6.0 0.9 - - + -
246M GLY 5.0 0.9 - - - -
247M CYS* 4.0 30.7 - - + +
250M GLU* 3.8 30.5 - - + -
316M LEU* 4.1 26.5 - - + -
319M LEU* 5.4 2.9 - - + -
323M LYS 3.3 6.8 + - - +
324M LEU* 3.3 27.0 + - + +
327M ARG* 1.3 104.0 - - + +
329M PRO* 1.4 62.8 - - - +
330M PHE 3.6 1.8 - - - -
331M ILE* 3.3 26.4 - - + +
332M CYS* 3.1 18.2 + - - +
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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