Contacts of the helix formed by residues 402 - 410 (chain A) in PDB entry 1XMI
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 GLU 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A PHE* 3.6 16.7 - - - +
401A TRP* 1.3 90.9 + - + +
403A GLU* 1.3 66.1 + - - +
404A GLY* 3.3 4.3 + - - +
405A PHE* 3.3 42.5 + - + -
406A GLY* 3.4 8.7 + - - -
437A GLY* 4.9 0.3 - - - -
438A THR* 4.2 20.2 + - - +
641D SER 6.1 0.4 - - - +
645D MET* 3.5 33.3 - - + +
649D SER* 4.7 4.5 - - - +
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Residues in contact with GLU 403 (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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400A PHE 5.6 0.7 - - - -
401A TRP 3.5 5.5 + - - +
402A GLU* 1.3 71.4 - - - +
404A GLY* 1.3 62.5 + - - +
406A GLY* 3.5 9.2 + - - +
407A GLU* 3.6 12.8 + - - +
584D LYS* 4.4 21.8 + - - +
606D LYS* 4.2 18.1 - - + +
607D MET* 4.1 24.3 + - + +
608D GLU* 4.0 33.6 + - - +
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Residues in contact with GLY 404 (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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402A GLU* 3.2 3.4 - - - +
403A GLU* 1.3 81.2 - - - +
405A PHE* 1.3 60.5 + - - +
406A GLY 3.5 0.2 + - - -
407A GLU* 3.8 2.9 + - - +
408A LEU* 3.6 15.4 + - - +
607D MET* 3.8 13.7 - - - +
641D SER* 3.3 43.5 + - - -
644D LEU* 5.9 1.6 - - - -
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Residues in contact with PHE 405 (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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400A PHE* 3.6 26.4 - + + -
402A GLU* 3.3 43.0 + - + +
404A GLY* 1.3 75.5 - - - +
406A GLY* 1.3 64.2 + - - +
408A LEU* 3.5 14.6 + - + +
409A PHE* 3.1 23.6 + - - +
433A PHE 4.8 0.4 - - - -
434A SER* 4.4 7.9 - - - +
436A LEU* 3.5 20.9 - - + -
437A GLY* 3.4 29.6 - - - -
641D SER 5.2 0.7 - - - -
642D SER* 3.5 31.0 - - - -
645D MET* 3.5 34.8 - - + -
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Residues in contact with GLY 406 (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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400A PHE* 3.8 11.8 - - - -
402A GLU 3.4 10.4 + - - -
403A GLU* 3.5 4.2 + - - -
404A GLY 3.3 1.0 - - - -
405A PHE* 1.3 77.9 - - - +
407A GLU* 1.3 61.5 + - - +
409A PHE* 3.1 17.8 + - - +
410A GLU* 3.4 6.6 + - - +
478A SER* 3.3 27.3 + - - -
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Residues in contact with GLU 407 (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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403A GLU 3.6 11.2 + - - +
404A GLY 4.2 6.3 - - - +
406A GLY* 1.3 73.8 - - - +
408A LEU* 1.3 62.5 + - + +
410A GLU* 3.1 24.6 + - - +
411A LYS* 4.0 3.6 + - - +
607D MET* 5.2 9.9 - - - -
611D LYS* 6.0 1.6 - - - +
634D GLN* 5.7 4.5 - - - +
641D SER* 5.7 2.0 - - - +
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Residues in contact with LEU 408 (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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404A GLY 3.6 9.8 + - - +
405A PHE* 3.5 21.5 + - + +
406A GLY 3.3 0.6 - - - -
407A GLU* 1.3 77.1 - - + +
409A PHE* 1.3 62.0 + - - +
411A LYS* 3.4 24.9 + - + +
433A PHE* 3.7 41.7 + - + +
434A SER* 3.9 18.7 + - - +
436A LEU* 5.4 0.2 - - + -
638D PRO* 3.6 21.8 - - + +
639D ASP 4.5 1.8 - - - +
641D SER* 3.7 26.2 - - - +
642D SER* 4.5 7.4 - - - +
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Residues in contact with PHE 409 (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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398A THR* 4.2 19.3 - - + -
400A PHE* 3.6 32.3 - + + -
405A PHE 3.1 12.8 + - - +
406A GLY 3.1 11.1 + - - +
408A LEU* 1.3 72.9 - - - +
410A GLU* 1.3 57.4 + - - +
411A LYS 3.0 15.7 + - - +
434A SER* 3.8 21.2 + - - -
439A PRO* 5.7 1.1 - - + -
442A LYS* 5.2 15.7 - - - -
478A SER* 4.6 12.8 - - - -
479A GLU* 3.9 31.2 - - + -
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Residues in contact with GLU 410 (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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406A GLY 3.4 6.8 + - - +
407A GLU* 3.1 16.7 + - - +
409A PHE* 1.3 77.6 - - - +
411A LYS* 1.3 57.9 + - - +
478A SER* 4.9 12.6 - - - +
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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