Contacts of the helix formed by residues 424 - 435 (chain D) in PDB entry 6B0Q
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 ARG 424 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400D THR* 3.8 32.1 + - + -
411D PHE* 3.3 14.6 - - + -
422D PHE* 3.4 3.4 - - - +
423D ALA* 1.3 83.4 - - - +
425D SER* 1.3 65.6 + - - +
426D ASP* 2.5 36.3 + - - +
427D GLU* 3.2 28.3 + - + +
428D LEU 3.3 8.7 + - - -
3E C 3.4 33.6 - - - +
4E G 2.9 48.9 + - - -
5E T 3.3 20.4 + - - +
9F C 5.9 0.2 - - - +
10F A 3.4 1.4 - - - +
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D PHE* 3.3 28.9 - - - -
424D ARG* 1.3 74.2 - - - +
426D ASP* 1.3 65.0 + - - +
428D LEU* 3.0 6.7 + - - +
429D VAL* 3.0 32.5 + - - +
8F C 3.2 50.7 + - - +
9F C 5.0 2.4 + - - -
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Residues in contact with ASP 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D ARG* 2.5 54.4 + - - +
425D SER* 1.3 79.4 + - - +
427D GLU* 1.3 59.4 + - - +
429D VAL* 3.8 10.8 - - - +
430D ARG* 3.1 23.7 + - - +
3E C 4.4 5.9 + - - -
4E G 4.4 0.5 - - - +
9F C 4.4 14.6 + - + -
10F A 3.0 29.8 + - - +
11F C 4.5 2.5 + - - +
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Residues in contact with GLU 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D PHE* 3.8 20.8 - - + +
423D ALA* 3.9 14.3 + - - +
424D ARG* 3.2 41.1 + - + +
425D SER 3.1 0.8 - - - -
426D ASP* 1.3 79.0 - - - +
428D LEU* 1.3 62.7 + - - +
430D ARG* 3.4 9.3 + - - +
431D HIS* 3.1 20.6 + - - +
2E G 3.0 57.0 + - + +
3E C 4.1 23.8 + - + +
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Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D PHE* 3.9 33.2 - - + -
412D SER 3.6 17.9 - - - +
413D CYS* 3.7 31.2 - - + +
422D PHE* 4.0 19.7 - - + -
424D ARG 3.3 2.0 + - - +
425D SER 3.0 9.4 + - - +
427D GLU* 1.3 75.6 - - - +
429D VAL* 1.3 62.7 + - + +
431D HIS* 3.1 2.8 + - + -
432D HIS* 2.8 52.2 + - + +
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Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D SER* 3.0 23.9 + - - +
426D ASP* 3.8 9.6 - - - +
427D GLU 3.3 0.2 - - - -
428D LEU* 1.3 78.7 - - + +
430D ARG* 1.3 61.5 + - - +
432D HIS* 3.2 10.6 + - + +
433D ASN* 2.8 42.7 + - - +
9F C 4.0 20.6 - - - +
10F A 5.9 2.0 - - - +
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Residues in contact with ARG 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D ASP 3.1 17.5 + - - +
427D GLU* 3.7 7.6 - - - +
428D LEU 3.3 0.2 - - - -
429D VAL* 1.3 75.6 - - - +
431D HIS* 1.3 61.5 + - - +
433D ASN* 3.4 9.8 + - - +
434D MET* 3.1 33.6 + - + +
2E G 2.5 37.1 + - - -
3E C 3.8 8.9 - - - +
11F C 4.4 9.5 - - - +
12F G 3.0 25.3 + - - -
13F C 4.6 4.0 - - - +
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Residues in contact with HIS 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D CYS* 3.5 17.2 - - + +
418D CYS* 3.7 5.8 - - - -
420D LYS* 4.3 7.9 - - + +
422D PHE* 3.5 36.7 - + + -
427D GLU 3.1 8.9 + - - +
428D LEU* 3.5 9.0 - - + +
430D ARG* 1.3 75.0 - - - +
432D HIS* 1.3 65.1 + - - +
434D MET* 3.2 9.4 + - + +
435D HIS* 2.7 43.6 + + - -
504D ZN 2.0 37.4 - - - -
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Residues in contact with HIS 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D CYS* 3.7 15.5 - - - -
414D ARG* 3.7 32.2 + - + +
415D TRP* 3.8 22.8 + + - +
428D LEU* 2.8 45.2 + - + +
429D VAL* 3.2 9.6 + - + +
431D HIS* 1.3 72.9 - - - +
433D ASN* 1.3 65.3 + - - +
435D HIS* 3.4 17.9 + - - +
436D GLN* 3.7 17.6 + - - +
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Residues in contact with ASN 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D VAL* 2.8 35.1 + - - +
430D ARG* 3.8 7.8 - - - +
431D HIS 3.2 0.2 - - - -
432D HIS* 1.3 78.9 + - - +
434D MET* 1.3 61.5 + - + +
435D HIS 3.1 5.2 - - - -
436D GLN* 3.2 31.7 + - - +
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Residues in contact with MET 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D ARG* 3.1 27.2 + - + +
431D HIS* 3.2 10.0 + - - +
433D ASN* 1.3 73.6 - - + +
435D HIS* 1.3 59.6 + - - +
436D GLN 3.1 9.3 + - - -
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Residues in contact with HIS 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D CYS* 4.3 3.1 - - - -
415D TRP* 3.4 63.0 - + + +
416D PRO 6.0 0.2 - - - -
418D CYS* 3.9 11.0 - - + -
431D HIS* 2.7 40.4 + + - -
432D HIS* 3.5 13.2 - - - +
433D ASN 3.1 1.4 - - - -
434D MET* 1.3 76.6 - - - +
436D GLN* 1.3 57.2 + - - +
504D ZN 2.0 35.6 - - - -
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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