Contacts of the helix formed by residues 337 - 343 (chain A) in PDB entry 5MLE
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 ASN 337 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.2 13.2 - - + +
336A PHE* 1.3 75.4 - - - +
338A THR* 1.3 58.6 + - - +
339A ALA* 3.1 21.8 + - - +
340A GLN* 3.1 38.4 + - - +
341A LYS* 2.9 26.8 + - - +
428A SER* 6.0 1.6 - - - +
429A LEU* 4.4 11.7 - - + -
430A GLU* 3.5 22.4 - - - +
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Residues in contact with THR 338 (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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295A TRP* 4.8 3.3 - - - -
296A ALA* 3.3 32.4 + - + +
337A ASN* 1.3 76.5 - - - +
339A ALA* 1.3 61.7 + - + +
341A LYS* 3.6 9.5 - - - +
342A ALA* 3.2 25.1 + - - +
430A GLU* 3.0 28.5 + - + +
431A TYR* 3.5 16.1 - - + -
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Residues in contact with ALA 339 (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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337A ASN* 3.1 9.1 + - - +
338A THR* 1.3 84.2 - - + +
340A GLN* 1.3 64.4 + - - +
342A ALA* 3.1 20.8 + - - +
343A VAL* 3.6 6.1 + - - +
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Residues in contact with GLN 340 (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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83A MET* 3.7 34.1 - - + +
84A THR 2.9 25.2 + - - +
86A ALA* 3.6 14.1 - - - +
336A PHE* 3.4 19.7 - - + -
337A ASN* 3.1 42.7 + - - +
339A ALA* 1.3 76.0 - - + +
341A LYS* 1.3 62.5 + - - +
342A ALA 3.3 0.5 + - - -
343A VAL* 3.4 23.7 - - - +
352A PRO* 3.6 10.5 - - - +
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Residues in contact with LYS 341 (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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295A TRP* 3.6 10.5 - - + -
296A ALA 5.7 1.3 - - - +
299A ALA* 3.3 39.5 + - + +
300A ALA* 4.2 8.9 + - - +
302A VAL* 3.3 11.1 + - - +
336A PHE* 3.7 26.0 - - + +
337A ASN 2.9 25.5 + - - +
338A THR* 3.6 10.1 - - - +
340A GLN* 1.3 73.6 - - - +
342A ALA* 1.3 56.3 + - - +
344A GLY 3.1 16.5 + - - -
351A ILE* 3.6 22.9 - - + +
352A PRO* 3.1 28.2 + - - +
353A GLU 4.4 0.2 - - - -
354A GLY 3.0 29.2 + - - +
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 3.7 17.7 - - + -
338A THR 3.2 12.3 + - - +
339A ALA* 3.1 16.1 + - - +
341A LYS* 1.3 74.1 - - - +
343A VAL* 1.3 65.2 + - - +
344A GLY 2.9 1.3 - - - -
345A LYS* 2.8 36.7 + - + +
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Residues in contact with VAL 343 (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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83A MET* 4.0 24.7 - - + -
339A ALA 3.6 5.5 + - - +
340A GLN* 3.4 19.9 + - - +
341A LYS 4.4 0.4 - - - +
342A ALA* 1.3 75.7 - - - +
344A GLY* 1.3 57.5 + - - +
345A LYS* 3.6 4.3 + - - +
346A ASP 5.1 0.3 + - - -
350A LEU* 3.9 34.5 - - + +
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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