Contacts of the helix formed by residues 428 - 446 (chain A) in PDB entry 6T2C
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 ALA 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 1.3 81.4 - - - +
429A PRO* 1.3 71.9 - - - +
430A ILE* 3.3 7.0 - - + +
431A GLU* 3.1 32.3 + - + +
432A HIS* 3.2 12.0 + - - -
130C PHE* 3.8 26.0 - - + -
234C LEU* 4.6 4.0 - - + -
242C GLN* 3.6 19.3 - - - +
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Residues in contact with PRO 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL 4.0 4.0 - - - +
428A ALA* 1.3 83.4 - - - +
430A ILE* 1.3 57.2 + - - +
432A HIS* 3.2 13.8 + - + +
433A ILE* 3.0 33.3 + - - +
130C PHE* 4.4 7.0 - - + -
131C GLY 3.4 20.2 - - - +
132C PRO* 4.9 1.8 - - + -
133C VAL* 3.8 25.1 - - + -
242C GLN* 3.3 18.6 - - - +
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Residues in contact with ILE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ALA* 4.5 2.5 - - + -
429A PRO* 1.3 79.4 - - - +
431A GLU* 1.3 61.6 + - + +
433A ILE* 4.3 18.2 - - + -
434A ALA* 2.9 28.9 + - - +
437A ARG* 5.6 1.8 - - - +
541B PRO* 3.8 23.5 - - + +
601B LEU* 5.0 6.5 - - + -
133C VAL* 4.3 15.6 - - + +
135C PHE* 5.8 1.3 - - + -
234C LEU* 4.0 28.0 - - + +
240C TRP* 3.9 39.7 - - + +
242C GLN* 3.3 23.4 + - - +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 3.4 12.5 - - + -
427A VAL 4.4 1.8 - - - -
428A ALA* 3.1 20.7 + - + +
430A ILE* 1.3 81.8 - - + +
432A HIS* 1.3 53.5 + - - +
434A ALA* 4.3 1.1 - - - -
435A SER* 2.7 38.3 + - - -
545B GLN* 3.7 10.5 + - - +
600B ASN* 2.4 33.7 + - - +
601B LEU* 3.2 19.6 + - + -
602B ARG* 2.8 58.1 + - - +
234C LEU* 5.2 0.7 - - + -
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Residues in contact with HIS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 3.4 34.9 + - + +
427A VAL 3.4 24.6 + - - -
428A ALA 3.2 9.4 + - - -
429A PRO* 3.2 13.2 + - + +
431A GLU* 1.3 74.6 - - - +
433A ILE* 1.3 59.9 + - - +
435A SER* 3.4 5.8 + - - -
436A ARG* 3.0 45.0 + - - +
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PRO 3.0 16.1 + - - +
430A ILE* 3.8 18.6 - - + +
432A HIS* 1.3 76.4 - - - +
434A ALA* 1.3 62.4 + - - +
436A ARG* 3.3 23.6 + - - +
437A ARG* 3.0 55.9 + - - +
601A ASP* 3.4 19.5 - - + +
603A THR* 3.6 10.5 - - + +
541B PRO* 6.3 0.2 - - + -
133C VAL* 4.3 15.3 - - + -
135C PHE* 4.1 19.1 - - + -
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Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE 2.9 18.7 + - - +
431A GLU* 3.7 0.7 - - - +
433A ILE* 1.3 78.3 - - - +
435A SER* 1.3 57.1 + - - +
437A ARG* 3.4 3.0 + - - +
438A ARG* 2.9 32.4 + - - +
541B PRO* 3.6 30.2 - - + +
542B ALA* 3.8 10.0 - - - +
545B GLN* 3.5 26.9 - - + +
601B LEU* 4.5 0.9 - - + -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 2.6 28.8 + - - -
431A GLU 2.7 17.8 + - - -
432A HIS* 3.7 7.6 - - - -
434A ALA* 1.3 75.6 - - - +
436A ARG* 1.3 58.0 + - - +
438A ARG* 4.0 13.7 + - - +
439A ASN* 2.9 40.5 + - - +
545B GLN* 3.7 13.0 + - - -
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Residues in contact with ARG 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A HIS* 3.0 27.0 + - - +
433A ILE* 3.5 30.9 - - - +
435A SER* 1.3 76.2 - - - +
437A ARG* 1.3 62.7 + - - +
439A ASN* 4.0 3.0 - - - +
440A PHE* 3.0 24.8 + - - +
601A ASP* 4.8 10.9 + - - -
603A THR* 4.5 17.1 - - + +
604A GLU* 3.6 29.7 + - - +
607A PHE* 4.9 1.1 - - - -
608A ARG* 6.4 0.4 - - - +
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE* 5.6 1.8 - - - +
433A ILE* 3.0 34.4 + - - +
434A ALA* 3.9 4.7 - - - +
436A ARG* 1.3 75.5 - - - +
438A ARG* 1.3 63.6 + - - +
440A PHE* 3.4 2.4 + - - +
441A PHE* 3.0 24.4 + - - +
584A LEU* 5.0 4.6 - - + +
588A GLU* 3.5 35.1 + - + +
591A ILE* 3.9 27.6 - - + +
592A GLU* 4.4 15.6 + - - +
595A SER* 5.2 3.8 + - - -
601A ASP* 4.4 3.6 + - - +
602A MET 5.9 0.4 - - - +
603A THR* 3.0 36.0 + - + -
607A PHE* 3.9 19.9 - - + -
541B PRO* 4.3 14.0 - - - +
542B ALA* 3.9 12.1 - - + -
135C PHE* 5.5 5.5 - - - -
240C TRP* 5.3 7.3 - - - +
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Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PHE* 6.1 0.2 - - - -
423A LEU* 3.6 17.4 - - - +
426A ASP* 5.2 1.4 + - - -
434A ALA 2.9 14.8 + - - +
435A SER* 4.0 13.1 + - - +
437A ARG* 1.3 76.9 - - - +
439A ASN* 1.3 88.9 + - - +
441A PHE* 3.4 5.3 + - - +
442A THR* 2.8 36.8 + - - +
584A LEU* 4.9 3.1 - - + -
542B ALA* 4.2 13.2 - - + +
545B GLN* 3.0 38.8 + - - +
546B MET* 4.0 28.0 - - + +
549B GLN* 3.3 33.2 + - - +
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Residues in contact with ASN 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A SER* 2.9 27.4 + - - +
436A ARG* 4.1 2.9 - - - +
438A ARG* 1.3 101.9 + - - +
440A PHE* 1.3 59.8 + - - +
442A THR* 4.3 6.0 - - - -
443A ALA* 3.0 31.4 + - - +
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Residues in contact with PHE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ARG 3.0 18.6 + - - +
437A ARG 3.8 1.1 - - - +
439A ASN* 1.3 76.4 - - - +
441A PHE* 1.3 66.2 + - - +
443A ALA* 3.3 6.6 + - + +
444A GLU* 3.0 53.0 + - + +
607A PHE* 3.4 73.6 - + + -
628A ILE* 4.2 18.6 - - + -
629A GLY 5.1 1.3 - - - -
632A CYS* 5.1 6.5 - - - -
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Residues in contact with PHE 441 (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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437A ARG 3.0 18.2 + - - +
438A ARG 3.8 3.4 - - - +
440A PHE* 1.3 83.1 - - + +
442A THR* 1.3 59.3 + - - +
444A GLU* 3.2 3.9 + - - +
445A VAL* 2.9 62.5 + - + +
580A LEU* 3.9 20.9 - - + -
583A SER* 3.2 28.5 - - - -
584A LEU* 3.9 35.9 - - + -
587A VAL* 4.9 5.8 - - + -
607A PHE* 5.8 2.9 - - + -
632A CYS* 3.7 40.8 - - + -
636A LEU* 5.1 1.1 - - + -
546B MET* 4.4 14.6 - - + -
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Residues in contact with THR 442 (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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418A ILE* 5.1 3.8 - - + +
420A PHE* 3.6 31.4 - - + -
438A ARG* 2.8 23.0 + - - +
439A ASN* 4.3 7.0 - - - -
441A PHE* 1.3 76.2 - - - +
443A ALA* 1.3 61.4 + - - +
444A GLU 3.5 0.3 + - - -
445A VAL* 4.2 7.6 - - + -
446A SER* 2.4 42.4 + - - +
546B MET* 3.4 21.3 - - - +
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASN 3.0 21.4 + - - +
440A PHE* 3.7 7.0 - - + +
442A THR* 1.3 78.3 - - - +
444A GLU* 1.3 67.1 + - - +
446A SER* 4.6 3.3 + - - -
447A GLN* 5.6 4.9 - - - +
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Residues in contact with GLU 444 (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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412A LEU* 4.4 9.2 - - - +
440A PHE* 3.0 46.3 + - + +
441A PHE* 3.9 4.0 - - - +
443A ALA* 1.3 87.0 - - - +
445A VAL* 1.3 59.9 + - - +
446A SER 3.7 0.4 - - - -
447A GLN 5.4 0.4 - - - -
629A GLY* 3.6 30.7 - - - -
632A CYS* 5.1 6.1 - - + -
633A ARG* 3.7 29.5 + - - +
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE* 5.5 0.9 - - + -
441A PHE* 2.9 53.5 + - + +
442A THR* 4.2 8.5 - - + -
443A ALA 3.5 0.2 - - - -
444A GLU* 1.3 78.7 - - - +
446A SER* 1.3 69.0 + - - +
447A GLN 3.5 1.7 + - - -
448A CYS* 3.7 11.3 + - + +
451A SER* 3.2 14.2 + - - -
580A LEU* 4.1 17.7 - - + -
632A CYS* 4.0 15.5 - - + +
633A ARG* 4.3 6.5 - - + -
636A LEU* 3.7 28.0 - - + -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASN* 4.1 23.9 + - - -
417A TRP* 3.4 18.5 - - - +
418A ILE* 4.0 20.1 + - - +
442A THR* 2.4 39.3 + - - +
443A ALA 4.6 2.4 + - - -
444A GLU 3.7 1.2 - - - -
445A VAL* 1.3 80.6 - - - +
447A GLN* 1.3 62.9 + - - +
448A CYS 3.1 5.2 + - - -
451A SER* 3.3 16.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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