Contacts of the helix formed by residues 617 - 636 (chain x) in PDB entry 5Z58
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 GLY 617 (chain x).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615x LEU* 5.2 0.2 - - - +
616x THR* 1.3 82.3 - - - +
618x GLN* 1.3 55.4 + - - -
619x GLU 3.2 2.9 - - - -
620x GLU* 2.9 8.4 + - - +
621x ILE* 2.7 36.7 + - - +
648x TYR* 5.4 2.7 - - - -
674x THR* 5.4 2.2 - - - -
696x LYS* 5.7 2.9 - - - -
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Residues in contact with GLN 618 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617x GLY* 1.3 71.6 - - - -
619x GLU* 1.3 63.2 + - - +
621x ILE* 4.3 6.3 - - - -
622x GLU* 3.3 26.7 + - - +
648x TYR* 4.8 15.0 - - + +
649x ALA 6.1 0.7 - - - +
650x ASN* 5.8 7.9 - - + -
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Residues in contact with GLU 619 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617x GLY 3.2 1.0 - - - -
618x GLN* 1.3 80.1 - - - +
620x GLU* 1.3 59.8 + - - +
622x GLU* 4.9 1.3 - - - +
623x ALA* 3.8 18.5 + - - +
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Residues in contact with GLU 620 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615x LEU* 5.5 4.3 - - + -
616x THR* 4.8 11.4 - - - +
617x GLY* 2.9 17.2 + - - +
619x GLU* 1.3 79.1 - - - +
621x ILE* 1.3 64.7 + - - +
623x ALA* 3.6 6.6 + - - +
624x ALA* 3.4 20.3 + - - +
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Residues in contact with ILE 621 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615x LEU* 5.1 13.9 - - + -
617x GLY 2.7 23.3 + - - +
618x GLN* 3.4 6.0 + - - +
620x GLU* 1.3 71.2 - - - +
622x GLU* 1.3 64.9 - - - +
624x ALA* 3.1 17.1 + - - +
625x CYS* 3.3 11.5 + - - +
646x PRO* 5.3 8.1 - - + +
647x ILE 5.0 4.9 - - - +
648x TYR* 4.8 13.0 - - + -
672x VAL* 4.9 14.1 - - - +
673x ALA* 5.4 4.3 - - - -
674x THR* 5.5 1.6 - - - +
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Residues in contact with GLU 622 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618x GLN 3.3 14.4 + - - +
619x GLU* 5.0 1.3 - - - +
621x ILE* 1.3 77.8 - - - +
623x ALA* 1.3 62.9 + - - +
625x CYS* 3.1 19.1 + - - +
626x GLU* 3.5 12.1 + - - +
646x PRO* 5.4 6.0 - - + +
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Residues in contact with ALA 623 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619x GLU 3.8 17.6 + - - +
620x GLU* 3.6 6.7 + - - +
621x ILE 3.2 1.0 - - - -
622x GLU* 1.3 77.7 - - - +
624x ALA* 1.3 60.3 + - - +
626x GLU* 3.9 2.6 + - - +
627x MET* 3.5 22.2 + - - +
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Residues in contact with ALA 624 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596x VAL* 6.0 6.1 - - + +
620x GLU 3.4 8.8 + - - +
621x ILE* 3.1 12.1 + - - +
623x ALA* 1.3 76.7 - - - +
625x CYS* 1.3 63.3 + - - +
627x MET* 4.0 5.7 - - - +
628x LEU* 3.3 24.9 + - - +
672x VAL* 5.1 11.2 - - + -
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Residues in contact with CYS 625 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621x ILE 3.3 9.3 + - - +
622x GLU* 3.1 14.4 + - - +
624x ALA* 1.3 77.7 - - - +
626x GLU* 1.3 59.4 + - + +
628x LEU* 3.5 2.8 + - - +
629x GLN* 2.9 29.6 + - - +
644x VAL* 4.9 11.8 - - + +
645x LEU* 5.6 1.1 - - - -
646x PRO* 4.7 19.1 - - + -
672x VAL* 5.2 9.0 - - + -
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Residues in contact with GLU 626 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622x GLU 3.5 9.6 + - - +
623x ALA* 4.9 1.8 - - - +
625x CYS* 1.3 76.7 - - - +
627x MET* 1.3 63.7 + - - +
629x GLN* 3.8 9.0 - - + +
630x ASP* 3.4 21.5 + - - +
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Residues in contact with MET 627 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596x VAL* 5.5 10.1 - - + -
623x ALA 3.5 18.1 + - - +
624x ALA* 4.2 6.3 - - - +
625x CYS 3.3 0.6 - - - -
626x GLU* 1.3 78.5 - - - +
628x LEU* 1.3 61.8 + - - +
630x ASP* 3.7 3.0 + - - +
631x ARG* 3.3 24.1 + - - +
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Residues in contact with LEU 628 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596x VAL* 5.6 11.2 - - + +
599x VAL* 6.2 3.8 - - + -
600x LEU* 6.1 6.3 - - + +
624x ALA 3.3 17.5 + - - +
625x CYS* 4.1 2.7 - - - +
627x MET* 1.3 77.4 - - - +
629x GLN* 1.3 56.0 + - - +
631x ARG* 4.8 3.6 - - - -
632x CYS* 2.6 36.0 + - - +
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Residues in contact with GLN 629 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625x CYS 2.9 20.0 + - - +
626x GLU* 4.0 9.0 - - + +
627x MET 3.3 0.2 - - - -
628x LEU* 1.3 78.3 - - - +
630x ASP* 1.3 59.7 + - - +
632x CYS* 2.9 23.6 - - - +
633x ARG* 3.2 8.1 + - - +
642x LEU 5.7 1.6 - - - -
644x VAL* 5.3 9.6 - - + +
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Residues in contact with ASP 630 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626x GLU 3.4 16.6 + - - +
627x MET* 4.1 3.6 - - - +
628x LEU 3.3 0.4 - - - -
629x GLN* 1.3 78.7 - - - +
631x ARG* 1.3 59.6 + - - +
633x ARG* 3.0 8.4 + - - +
634x ARG* 2.9 24.8 + - - +
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Residues in contact with ARG 631 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600x LEU* 5.3 14.8 - - + +
627x MET 3.3 16.5 + - - +
628x LEU* 4.3 3.6 - - - +
630x ASP* 1.3 74.6 - - - +
632x CYS* 1.3 60.9 + - - +
634x ARG* 3.6 12.6 - - + +
635x LEU* 2.9 28.1 + - - +
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Residues in contact with CYS 632 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600x LEU* 6.0 2.4 - - - +
628x LEU 2.6 25.2 + - - +
629x GLN* 2.9 17.7 - - - +
631x ARG* 1.3 75.0 - - - +
633x ARG* 1.3 54.9 + - - +
635x LEU* 3.3 7.1 + - - +
636x GLY* 3.0 20.1 + - - -
639x ILE* 5.2 0.2 - - - +
640x ARG 5.1 2.9 - - - +
641x GLU* 6.1 0.2 - - - -
642x LEU* 3.4 40.0 + - + +
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Residues in contact with ARG 633 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629x GLN 3.2 5.9 + - - +
630x ASP* 3.0 8.0 + - - +
632x CYS* 1.3 75.1 - - - +
634x ARG* 1.3 62.2 + - - +
635x LEU 3.1 1.8 - - - -
636x GLY* 2.8 28.1 + - - +
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Residues in contact with ARG 634 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630x ASP 2.9 14.2 + - - +
631x ARG* 3.7 16.2 - - + +
633x ARG* 1.3 76.8 - - - +
635x LEU* 1.3 60.5 + - - +
636x GLY 4.5 1.7 - - - -
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Residues in contact with LEU 635 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600x LEU* 5.5 9.2 - - + +
603x HIS* 5.9 5.4 - - + -
604x VAL* 6.2 2.7 - - + -
631x ARG 2.9 14.8 + - - +
632x CYS* 3.4 10.5 - - - +
634x ARG* 1.3 76.1 - - - +
636x GLY* 1.3 61.0 + - - +
639x ILE* 2.9 33.0 + - + +
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Residues in contact with GLY 636 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632x CYS 3.0 11.1 + - - -
633x ARG* 2.8 21.2 + - - -
634x ARG 4.5 1.8 - - - -
635x LEU* 1.3 82.1 - - - +
639x ILE* 3.4 31.6 + - - +
640x ARG 5.2 2.0 - - - -
641x GLU* 6.0 1.6 - - - -
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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