Contacts of the helix formed by residues 294 - 301 (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 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A SER* 3.3 12.2 + - - +
293A LYS* 1.3 77.0 - - - +
295A TRP* 1.3 63.1 + - - +
296A ALA* 3.1 17.8 + - - +
297A LYS* 3.1 20.8 + - + +
298A ALA* 3.2 11.4 + - - +
431A TYR* 2.7 35.4 + - - -
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Residues in contact with TRP 295 (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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218A THR 5.5 0.4 + - - -
219A GLY* 4.6 5.2 - - - -
220A PRO* 3.6 29.7 - - + +
292A SER 5.0 1.1 - - - -
293A LYS 3.3 6.8 + - - -
294A ASN* 1.3 72.1 + - - +
296A ALA* 1.3 67.2 + - + +
297A LYS 3.1 0.3 + - - -
298A ALA* 3.2 7.8 + - - +
299A ALA* 2.9 48.0 + - + +
338A THR 4.8 2.2 - - - -
341A LYS* 3.6 25.8 - - + -
342A ALA* 3.7 26.2 - - + -
344A GLY 3.4 9.2 + - - -
345A LYS* 3.4 40.3 + - + -
351A ILE* 3.8 13.7 - - + -
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Residues in contact with ALA 296 (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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294A ASN* 3.1 11.8 + - - +
295A TRP* 1.3 91.9 - - + +
297A LYS* 1.3 57.3 + - - +
299A ALA* 3.7 4.2 - - - +
300A ALA* 3.2 24.4 + - - +
338A THR* 3.3 27.7 + - + +
341A LYS* 5.7 1.4 - - - +
431A TYR* 3.7 19.5 - - + +
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Residues in contact with LYS 297 (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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289A HIS* 3.7 30.9 + - - -
292A SER* 3.5 18.6 + - - +
294A ASN* 3.1 28.8 + - + +
296A ALA* 1.3 74.7 - - - +
298A ALA* 1.3 69.0 + - - +
299A ALA 3.1 0.9 - - - -
300A ALA* 2.8 15.8 + - + +
301A PHE* 3.3 29.0 - - + -
431A TYR* 3.9 20.9 - - + -
435A GLU* 6.3 3.1 - - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PRO* 3.6 18.8 - - + -
289A HIS 3.4 19.4 + - - +
290A TYR* 3.5 36.4 - - - +
292A SER* 4.1 9.6 - - - +
294A ASN 3.2 8.2 + - - +
295A TRP* 3.5 9.4 - - - +
297A LYS* 1.3 76.4 - - - +
299A ALA* 1.3 61.2 + - - +
301A PHE* 3.2 19.8 + - - +
302A VAL* 3.9 1.7 - - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PRO* 4.0 3.7 - - + +
295A TRP* 2.9 49.2 + - + +
296A ALA 3.7 6.3 - - - +
298A ALA* 1.3 72.3 - - - +
300A ALA* 1.3 62.3 + - - +
301A PHE 3.0 6.6 + - - -
302A VAL* 3.1 21.7 + - - +
341A LYS* 3.3 29.6 + - + +
351A ILE* 4.7 3.6 - - + -
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Residues in contact with ALA 300 (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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296A ALA 3.2 14.1 + - - +
297A LYS* 2.8 17.4 + - + +
299A ALA* 1.3 70.8 - - - +
301A PHE* 1.3 59.1 + - + +
302A VAL 3.6 0.2 + - - -
341A LYS* 4.4 10.9 - - + +
354A GLY 3.7 7.1 - - - +
355A THR* 3.0 19.9 + - - -
429A LEU* 6.2 3.6 - - + -
431A TYR* 3.9 26.7 - - + -
432A ASN 5.9 0.2 - - - -
433A ILE* 3.8 13.8 - - + +
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Residues in contact with PHE 301 (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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285A THR* 4.0 12.6 - - + -
286A ASP 4.1 5.2 - - - -
287A GLY* 5.6 0.9 - - - -
289A HIS* 3.3 50.5 - + + -
290A TYR* 2.8 33.9 + + + -
297A LYS* 3.3 37.5 - - + -
298A ALA* 3.2 10.9 + - - +
299A ALA 3.0 1.2 - - - -
300A ALA* 1.3 79.2 - - + +
302A VAL* 1.3 62.1 + - - +
303A THR* 3.1 11.1 + - - +
307A LEU* 3.5 24.9 - - + +
355A THR* 4.1 4.7 + - - -
432A ASN 5.3 0.9 - - - -
433A ILE* 3.4 47.1 - - + -
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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