Contacts of the helix formed by residues 398 - 407 (chain A) in PDB entry 1ZD4
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 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A GLU 4.2 2.2 + - - +
395A LEU 3.8 1.8 + - - -
397A GLN* 1.3 92.3 + - - +
399A LEU* 1.3 51.3 + - - +
400A SER* 3.5 9.9 + - - -
401A ARG* 2.7 47.3 + - + +
402A THR* 2.8 36.1 + - - +
433A GLU* 4.4 15.3 + - - +
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Residues in contact with LEU 399 (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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395A LEU 3.8 14.8 - - - +
396A GLU* 3.9 20.2 - - + +
397A GLN 4.0 0.4 - - - -
398A ASN* 1.3 70.8 - - - +
400A SER* 1.3 65.3 + - - +
402A THR* 3.0 6.0 + - - -
403A PHE* 3.0 37.2 + - + -
450A VAL* 3.4 39.0 - - + +
453A PHE* 4.3 9.4 - - + +
454A LYS* 3.5 29.8 - - + +
458A PHE* 4.0 20.9 - - + -
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Residues in contact with SER 400 (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 ASN* 3.3 7.8 - - - -
399A LEU* 1.3 77.4 - - - +
401A ARG* 1.3 62.5 + - - +
403A PHE* 3.7 1.6 + - - +
404A LYS* 3.1 45.1 + - - +
446A ILE* 4.4 1.0 - - - +
447A GLN* 3.6 23.8 + - - +
450A VAL* 3.9 15.9 - - - +
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Residues in contact with ARG 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 GLN* 5.7 4.8 - - - +
398A ASN* 2.7 35.3 + - - +
400A SER* 1.3 70.9 - - - +
402A THR* 1.3 63.8 + - - +
404A LYS* 3.2 5.3 + - - +
405A SER* 2.6 42.5 + - - +
428A PHE* 3.3 51.1 + - + +
431A SER* 2.8 31.7 + - - -
432A PRO 2.9 15.3 + - - -
433A GLU* 3.8 35.8 + - - +
435A PRO* 3.9 15.5 - - + -
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Residues in contact with THR 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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394A GLU 4.2 0.5 + - - -
395A LEU* 2.7 51.5 + - + +
398A ASN 2.8 15.7 + - - -
399A LEU* 3.3 9.9 - - - -
401A ARG* 1.3 74.1 - - - +
403A PHE* 1.3 60.0 + - + +
405A SER* 3.4 2.1 + - - -
406A LEU* 3.1 44.4 + - + +
428A PHE* 3.5 23.2 - - + -
458A PHE* 4.0 17.0 - - + -
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Residues in contact with PHE 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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266A PRO* 3.7 22.4 - - + -
399A LEU* 3.0 36.5 + - + +
400A SER 4.3 1.8 - - - +
402A THR* 1.3 72.6 - - - +
404A LYS* 1.3 61.8 + - - +
405A SER 3.1 2.2 - - - -
406A LEU* 4.4 7.9 - - + +
407A PHE* 3.0 62.2 + + + +
446A ILE* 4.0 14.1 - - + +
449A TYR* 3.8 29.2 - - + -
450A VAL* 4.0 12.8 - - + -
453A PHE* 3.3 36.6 - + + -
458A PHE* 3.7 22.2 - + - -
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Residues in contact with LYS 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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400A SER* 3.1 34.1 + - - +
401A ARG* 3.8 5.8 - - - +
403A PHE* 1.3 76.5 - - - +
405A SER* 1.3 58.5 + - - +
407A PHE 4.2 3.7 - - - +
408A ARG* 3.1 30.0 + - - +
435A PRO* 4.3 23.1 + - + +
436A SER 4.1 15.5 + - - +
437A LEU* 4.5 14.3 - - + +
438A SER* 5.2 2.5 + - - +
441A VAL* 6.1 0.4 - - - -
443A GLU* 2.9 40.1 + - - -
446A ILE* 4.0 25.6 - - + -
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Residues in contact with SER 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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401A ARG* 2.6 32.5 + - - +
402A THR 3.6 3.6 - - - -
404A LYS* 1.3 79.0 - - - +
406A LEU* 1.3 64.3 + - - +
408A ARG* 3.6 12.9 - - - +
415A VAL* 3.7 17.0 + - - +
416A LEU* 3.4 31.0 - - - +
428A PHE* 4.2 10.1 - - - -
431A SER* 5.0 2.8 - - - -
435A PRO* 3.2 19.2 - - - +
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Residues in contact with LEU 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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265A PHE* 5.5 2.0 - - + -
266A PRO* 3.6 34.1 - - + -
395A LEU* 5.0 5.2 - - + -
402A THR* 3.1 37.1 + - + +
403A PHE* 4.0 7.4 - - + +
405A SER* 1.3 80.2 - - - +
407A PHE* 1.3 57.6 + - + +
408A ARG* 2.7 20.4 + - - +
416A LEU* 3.4 23.6 - - + -
418A MET* 5.9 1.1 - - + -
427A LEU* 4.4 15.3 - - + -
428A PHE* 5.1 0.4 - - + -
524A TRP* 3.0 31.5 + - + -
700A NC6 5.3 14.5 + - + +
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Residues in contact with PHE 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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266A PRO* 3.7 14.6 - - + -
267A GLU* 4.1 3.4 - - + -
403A PHE* 3.0 38.0 + + + +
404A LYS* 4.2 3.8 - - - +
406A LEU* 1.3 73.5 - - + +
408A ARG* 1.3 62.3 + - - +
438A SER* 3.0 21.8 - - - -
440A MET* 3.5 5.5 - - + +
441A VAL* 4.5 7.9 - - + +
446A ILE* 3.9 17.0 - - + -
449A TYR* 3.5 48.0 - + - -
524A TRP* 3.4 46.9 - + - +
527A MET* 3.7 28.5 - - + -
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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