Contacts of the helix formed by residues 400 - 409 (chain A) in PDB entry 4Y2P
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A GLU 4.6 1.2 + - - -
397A LEU 4.4 0.8 + - - -
399A GLN* 1.3 95.8 + - - +
401A LEU* 1.3 59.3 + - - +
402A SER* 3.5 9.4 + - - -
403A ARG* 3.1 39.6 + - + +
404A THR* 2.9 27.8 + - - -
434A GLU* 4.2 13.1 + - - -
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Residues in contact with LEU 401 (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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397A LEU 3.8 8.3 - - - +
398A GLU* 4.2 16.2 - - + +
400A ASN* 1.3 71.7 + - - +
402A SER* 1.3 62.8 + - - +
404A THR* 3.1 4.3 + - - -
405A PHE* 2.9 35.0 + - + -
451A VAL* 3.8 31.4 - - + +
454A PHE* 4.2 12.6 - - + +
455A LYS* 3.7 40.4 - - + +
459A PHE* 3.5 32.5 - - + -
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Residues in contact with SER 402 (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 ASN* 3.5 7.6 + - - -
401A LEU* 1.3 79.1 - - - +
403A ARG* 1.3 61.6 + - - +
405A PHE 3.5 0.2 + - - -
406A LYS* 2.9 50.6 + - - +
444A GLU* 4.5 0.2 + - - -
447A ILE* 4.1 3.1 - - - +
448A GLN* 3.8 20.4 + - - -
451A VAL* 3.6 15.0 - - - +
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Residues in contact with ARG 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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396A GLU* 5.8 2.6 + - - +
399A GLN* 5.2 8.1 + - - +
400A ASN* 3.1 33.3 + - - +
402A SER* 1.3 76.1 - - - +
404A THR* 1.3 58.0 + - - +
406A LYS* 4.4 1.1 - - - -
407A SER* 2.6 45.2 + - - +
429A PHE* 3.1 45.1 + - + +
432A SER* 2.8 29.7 + - - -
433A PRO 2.9 14.6 + - - -
434A GLU* 3.4 45.0 + - - +
436A PRO* 4.2 11.9 - - + -
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Residues in contact with THR 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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396A GLU 4.1 1.6 + - - -
397A LEU* 2.7 41.0 + - + -
400A ASN 2.9 13.0 + - - -
401A LEU* 3.1 10.3 + - - -
403A ARG* 1.3 78.5 - - - +
405A PHE* 1.3 68.6 + - + +
407A SER* 3.8 1.0 - - - -
408A LEU* 3.0 43.8 + - + +
429A PHE* 3.5 21.8 - - + -
459A PHE* 4.0 17.9 - - + -
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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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268A PRO* 3.5 27.6 - - + -
401A LEU* 2.9 47.1 + - + +
402A SER 4.5 1.1 - - - +
404A THR* 1.3 77.4 - - + +
406A LYS* 1.3 59.6 + - - +
408A LEU* 4.5 3.6 - - + +
409A PHE* 2.9 61.9 + + + +
447A ILE* 3.9 19.7 - - + +
450A TYR* 3.9 21.8 - - + -
451A VAL* 4.2 8.7 - - + -
454A PHE* 3.3 39.3 - + - -
459A PHE* 3.7 19.5 - + - -
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Residues in contact with LYS 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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402A SER* 2.9 35.3 + - - +
403A ARG* 4.0 2.7 - - - +
405A PHE* 1.3 81.0 - - - +
407A SER* 1.3 60.1 + - - +
409A PHE 4.1 3.5 - - - +
410A ARG* 2.9 29.7 + - - +
436A PRO* 4.0 34.5 + - + +
437A SER 4.6 5.6 - - - +
438A LEU* 4.3 17.5 - - + +
439A SER* 5.5 1.2 + - - +
442A VAL* 6.1 0.4 - - - -
444A GLU* 2.8 38.9 + - - -
447A ILE* 3.9 23.3 - - + +
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Residues in contact with SER 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 ARG* 2.6 36.0 + - - +
406A LYS* 1.3 72.1 - - - +
408A LEU* 1.4 63.8 + - - +
410A ARG* 3.4 14.2 - - - +
416A VAL* 3.9 18.1 - - - +
417A LEU* 3.8 17.8 + - - +
429A PHE* 3.7 28.4 - - - -
432A SER* 4.5 6.5 - - - -
436A PRO* 3.4 15.5 - - - +
602A 3C5 5.2 0.9 - - - -
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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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267A PHE* 5.6 1.1 - - + -
268A PRO* 3.6 32.3 - - + -
397A LEU* 4.7 4.5 - - + -
404A THR* 3.0 35.7 + - + +
405A PHE* 4.1 5.2 - - + +
407A SER* 1.4 78.4 - - - +
409A PHE* 1.3 65.6 + - + +
410A ARG* 3.0 8.3 + - - +
417A LEU* 3.9 13.9 - - + -
428A LEU* 4.5 6.3 - - + -
429A PHE* 4.2 11.0 - - + -
525A TRP* 2.8 30.4 + - + -
602A 3C5 3.8 45.4 - - + -
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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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268A PRO* 3.9 11.2 - - + -
269A GLU* 4.3 5.8 - - + -
405A PHE* 2.9 52.7 + + + +
406A LYS* 4.1 3.6 - - - +
407A SER 3.7 0.4 - - - -
408A LEU* 1.3 75.8 - - + +
410A ARG* 1.3 63.2 + - - +
439A SER* 3.2 21.7 + - - -
441A MET* 3.5 11.0 - - + +
442A VAL* 4.1 11.1 - - + +
447A ILE* 4.4 8.1 - - + -
450A TYR* 3.7 43.7 - + - -
525A TRP* 3.5 45.8 - + - +
528A MET* 4.0 18.6 - - + -
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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