Contacts of the helix formed by residues 627 - 639 (chain B) in PDB entry 4N41
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 PRO 627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625B ASP 3.6 7.8 - - - +
626B THR* 1.3 95.1 - - + +
628B LEU* 1.3 66.2 + - - +
629B GLU* 3.5 15.7 - - - +
630B ALA* 3.1 21.8 + - + +
631B LEU* 3.2 10.0 + - - +
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Residues in contact with LEU 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B TYR* 3.2 21.0 - - + +
595B PRO* 5.4 5.8 - - + -
599B LYS* 4.3 25.6 - - + +
600B THR 4.5 7.6 - - - +
601B PHE* 3.6 35.0 - - + -
621B HIS* 3.6 36.5 + - + +
626B THR 3.7 1.4 + - - -
627B PRO* 1.3 70.7 - - - +
629B GLU* 1.3 62.0 + - - +
631B LEU* 3.2 7.2 + - + +
632B ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TYR* 5.6 6.9 - - + -
316B LEU* 4.8 6.0 - - + +
593B TYR* 3.3 39.0 + - + -
595B PRO* 5.7 0.2 - - - +
627B PRO* 3.5 20.1 - - + +
628B LEU* 1.3 79.6 + - - +
630B ALA* 1.3 57.0 + - - +
632B ALA* 3.4 2.5 + - - +
633B HIS* 2.9 31.0 + - - +
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Residues in contact with ALA 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B PRO* 4.2 17.5 - - + +
626B THR* 3.7 17.3 - - + -
627B PRO* 3.1 19.1 + - + +
629B GLU* 1.3 78.8 + - - +
631B LEU* 1.3 58.2 + - - +
633B HIS* 3.4 7.5 + - - +
634B GLN* 2.9 30.0 + - - +
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Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 3.8 29.2 - - + -
569B ASP* 3.9 8.7 - - + +
571B VAL* 4.0 9.0 - - + -
601B PHE* 4.9 4.9 - - + -
621B HIS* 3.4 48.2 - - + +
626B THR* 3.8 24.7 - - + +
627B PRO 3.2 10.2 + - - +
628B LEU* 3.4 14.8 - - + +
630B ALA* 1.3 73.2 - - - +
632B ALA* 1.3 61.2 + - - +
634B GLN* 3.2 7.4 + - - +
635B ILE* 2.9 41.7 + - + +
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Residues in contact with ALA 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 3.6 5.1 - - + +
593B TYR* 3.6 22.2 - - + -
601B PHE* 3.6 30.0 - - + -
603B LEU* 3.8 13.3 - - + +
628B LEU 2.9 19.6 + - - +
629B GLU 3.8 3.1 - - - +
631B LEU* 1.3 73.0 - - - +
633B HIS* 1.3 57.1 + - - +
635B ILE* 4.5 1.6 - - - -
636B PHE* 2.9 34.0 + - - +
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Residues in contact with HIS 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.0 18.8 - - + +
317B SER* 2.8 37.2 + - - -
468B ALA 5.3 3.1 - - - -
469B TYR* 3.8 18.1 - + - -
470B PRO* 6.2 0.6 - - - +
629B GLU 2.9 18.6 + - - +
630B ALA* 3.5 8.4 + - - +
632B ALA* 1.3 77.6 - - - +
634B GLN* 1.3 62.5 + - - +
636B PHE* 3.8 0.7 - - - +
637B HIS* 2.9 62.1 + + - +
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Residues in contact with GLN 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B LEU* 5.4 0.4 - - + +
469B TYR* 3.6 33.5 - - + +
470B PRO* 3.5 12.5 - - + +
471B ALA* 2.8 49.4 + - - +
474B ALA* 4.9 5.7 - - - +
542B LEU* 4.0 17.2 - - + +
630B ALA 2.9 17.2 + - - +
631B LEU* 3.7 6.4 - - - +
633B HIS* 1.3 79.0 + - - +
635B ILE* 1.3 57.5 + - - +
637B HIS* 3.4 2.1 + - - +
638B LEU* 2.9 51.1 + - + +
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Residues in contact with ILE 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 4.1 17.3 - - + -
544B LEU* 4.0 21.3 - - + -
571B VAL* 4.1 14.4 - - + -
573B VAL* 5.2 0.9 - - + -
601B PHE* 4.8 0.2 - - + -
603B LEU* 4.1 14.6 - - + -
617B LEU* 5.7 1.8 - - + -
619B LEU* 3.5 30.1 - - + -
631B LEU* 2.9 27.8 + - + +
632B ALA* 4.0 3.8 - - - +
634B GLN* 1.3 72.1 - - - +
636B PHE* 1.3 68.0 + - - +
638B LEU* 3.0 19.1 + - - +
639B THR* 3.1 14.4 + - + +
653B PRO* 3.7 29.4 - - + +
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Residues in contact with PHE 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 3.8 28.0 - - + -
317B SER 3.9 7.2 - - - -
318B ILE* 5.1 0.9 - - - -
319B PRO* 3.8 23.1 - - + -
590B ASP* 4.5 2.9 - - + -
591B GLY* 3.5 27.6 - - - -
603B LEU* 4.0 9.8 - - + +
605B THR* 3.3 24.5 - - + -
632B ALA 2.9 18.2 + - - +
633B HIS 3.8 1.1 - - - +
635B ILE* 1.3 77.4 - - - +
637B HIS* 1.3 74.7 + + - +
639B THR* 2.8 33.0 + - - -
640B ARG* 3.2 43.1 + - - +
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Residues in contact with HIS 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER* 2.8 28.6 + - - -
318B ILE 4.3 2.0 - - - -
319B PRO* 3.4 37.8 - - + +
320B LYS 4.9 0.9 - - - -
465B LEU* 3.5 20.2 - - + +
469B TYR* 2.3 38.3 + + + +
633B HIS* 2.9 49.0 + + - +
634B GLN 3.7 3.6 - - - +
636B PHE* 1.3 85.5 - + - +
638B LEU* 1.3 61.5 + - - +
640B ARG* 3.1 19.2 + - - +
641B LEU 4.2 1.0 + - - -
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Residues in contact with LEU 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B LEU* 4.5 6.5 - - + -
474B ALA* 3.8 25.4 - - + -
494B VAL* 4.3 14.4 - - + -
542B LEU* 4.3 7.2 - - + -
544B LEU* 4.4 11.0 - - + -
634B GLN* 2.9 40.1 + - + +
635B ILE* 3.0 14.8 + - - +
637B HIS* 1.3 77.2 - - - +
639B THR* 1.3 59.9 + - - +
640B ARG 3.2 0.7 + - - -
641B LEU* 3.3 27.4 + - + +
653B PRO* 3.9 9.4 - - + -
654B ALA* 3.1 27.5 + - - +
655B PRO* 4.3 14.1 - - + -
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Residues in contact with THR 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B THR* 3.9 15.5 - - + -
635B ILE 3.1 11.1 + - - +
636B PHE* 2.8 18.0 + - - +
638B LEU* 1.3 77.7 - - - +
640B ARG* 1.3 87.8 + - - +
641B LEU 3.3 1.5 + - - -
642B TYR* 4.2 1.6 + - - +
649B PHE* 4.1 0.7 - - - +
650B PRO* 3.3 42.4 - - - +
651B ARG 3.7 20.6 - - - +
652B LEU 3.7 13.5 - - - +
653B PRO* 3.9 5.8 - - + -
654B ALA* 4.2 0.9 + - - +
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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