Contacts of the helix formed by residues 612 - 627 (chain I) in PDB entry 1DE4
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 GLU 612 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LYS* 5.5 8.8 - - - +
74G HIS* 5.4 1.9 + - - -
610I ASP* 3.0 21.7 + - - +
611I TYR* 1.3 90.1 - - + +
613I ARG* 1.3 67.4 + - + +
614I TYR 2.9 1.6 + - - -
615I ASN* 2.9 44.5 + - - +
616I SER* 4.3 6.8 + - - -
650I PHE* 4.0 17.3 - - - -
653I THR* 4.2 7.4 + - - -
657I THR* 5.5 3.4 - - - +
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Residues in contact with ARG 613 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500I PRO* 3.2 35.6 - - + +
503I TYR* 3.5 27.7 - - + +
504I THR* 2.9 39.0 + - - +
507I GLU* 3.4 25.1 + - - +
528I TRP* 4.9 1.2 - - - -
529I ALA* 4.0 20.0 - - - +
610I ASP* 3.1 23.0 + - + +
612I GLU* 1.3 80.8 - - - +
614I TYR* 1.3 59.2 - - - +
615I ASN 3.2 1.0 + - - -
616I SER* 3.4 19.4 + - - +
617I GLN* 3.7 12.0 + - - +
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Residues in contact with TYR 614 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500I PRO* 3.6 26.3 - - + +
501I LEU* 3.8 33.9 - - + -
611I TYR 3.4 3.9 + - - +
612I GLU 2.9 1.6 + - - -
613I ARG* 1.3 75.2 - - - +
615I ASN* 1.3 64.8 + - - +
616I SER 3.2 0.4 - - - -
617I GLN* 3.7 10.2 - - + +
618I LEU* 3.0 26.7 + - - +
649I PHE* 3.6 23.6 - - + -
681I VAL* 4.4 6.3 - - + -
682I GLU* 2.7 29.4 + - - -
685I PHE* 3.2 36.1 - + + -
699I HIS* 3.5 2.1 + - - -
701I PHE* 3.8 30.3 - + - -
702I TRP* 3.2 19.5 + - - -
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Residues in contact with ASN 615 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G HIS* 3.7 6.6 - - + +
612I GLU* 2.9 42.7 + - - +
614I TYR* 1.3 79.8 - - - +
616I SER* 1.3 56.9 + - - +
618I LEU* 3.4 6.3 + - - +
619I LEU* 3.0 29.6 + - - +
646I ARG* 4.4 3.3 + - - +
649I PHE* 3.7 8.7 - - - -
650I PHE* 3.1 55.9 + - + +
653I THR* 3.2 24.4 + - - +
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Residues in contact with SER 616 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 3.7 13.2 - - - +
74G HIS* 4.0 16.3 + - - -
612I GLU* 4.7 7.4 + - - -
613I ARG* 3.4 13.9 + - - -
614I TYR 3.2 0.6 - - - -
615I ASN* 1.3 80.1 - - - +
617I GLN* 1.3 58.5 + - - +
619I LEU* 4.5 1.6 - - - -
620I SER* 3.0 27.5 + - - -
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Residues in contact with GLN 617 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500I PRO* 3.5 32.9 - - + +
503I TYR* 4.0 16.6 + - - -
529I ALA 5.9 0.4 + - - -
613I ARG 3.9 9.6 - - - +
614I TYR* 3.4 13.6 + - + +
615I ASN 3.2 0.4 - - - -
616I SER* 1.3 76.7 - - - +
618I LEU* 1.3 64.7 + - - +
620I SER* 3.3 8.6 + - - -
621I PHE* 3.0 22.0 + - - +
701I PHE* 3.8 24.1 - - + -
702I TRP* 3.7 27.1 - - + -
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Residues in contact with LEU 618 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614I TYR 3.0 13.8 + - - +
615I ASN* 3.7 6.1 - - - +
617I GLN* 1.3 77.7 - - - +
619I LEU* 1.3 62.7 + - - +
621I PHE* 2.9 19.7 + - + +
622I VAL* 3.0 16.7 + - - +
646I ARG* 3.9 26.7 - - + +
649I PHE* 3.7 44.2 - - + -
685I PHE* 5.0 4.3 - - + -
701I PHE* 3.1 34.1 - - + -
709I LEU* 5.2 1.1 - - + -
742I ILE* 4.0 30.1 - - + -
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Residues in contact with LEU 619 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 3.6 24.2 - - + -
23G SER* 4.0 18.4 - - - +
74G HIS* 3.6 51.4 - - + +
77G THR* 4.4 3.4 - - + -
78G VAL* 3.5 30.7 - - + -
81G TRP* 3.6 19.7 - - + -
615I ASN 3.0 18.1 + - - +
616I SER 3.9 0.7 - - - +
618I LEU* 1.3 75.7 - - - +
620I SER* 1.3 58.1 + - - +
622I VAL* 3.0 9.6 + - - +
623I ARG 2.9 23.0 + - - -
646I ARG* 4.7 7.7 - - - +
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Residues in contact with SER 620 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 3.7 16.3 - - - +
616I SER 3.0 19.5 + - - -
617I GLN* 3.5 11.5 + - - -
618I LEU 3.2 0.2 - - - -
619I LEU* 1.3 77.8 - - - +
621I PHE* 1.3 56.0 + - - +
623I ARG* 3.2 15.9 + - - +
624I ASP* 2.9 39.9 + - - +
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Residues in contact with PHE 621 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617I GLN 3.0 11.8 + - - +
618I LEU* 2.9 14.4 + - + +
620I SER* 1.3 77.4 - - - +
622I VAL* 1.3 63.0 + - + +
624I ASP* 3.3 8.8 + - - +
625I LEU* 3.2 33.2 + - + +
642I LEU* 3.6 38.6 - - + -
701I PHE* 5.3 1.6 - - + -
709I LEU* 3.6 62.8 - - + -
712I LEU* 4.1 17.7 - - + -
713I LEU* 4.2 23.8 - - + -
735I LEU* 6.2 0.4 - - + -
738I ALA* 5.3 2.2 - - + -
742I ILE* 4.9 5.4 - - + -
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Residues in contact with VAL 622 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G VAL* 3.8 21.5 - - + -
81G TRP* 3.9 11.0 - - + -
618I LEU 3.0 16.1 + - - +
619I LEU* 3.3 10.1 - - - +
621I PHE* 1.3 80.6 - - + +
623I ARG* 1.3 61.2 + - - +
625I LEU* 3.2 16.0 + - - +
626I ASN* 3.3 13.4 + - - +
642I LEU* 4.7 13.0 - - + -
643I TYR* 3.4 37.2 + - + +
646I ARG* 4.1 26.0 - - + -
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Residues in contact with ARG 623 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G LEU 5.4 1.2 + - - -
21G GLY* 4.3 3.2 - - - -
22G LEU* 3.3 43.2 - - - +
81G TRP* 3.3 44.6 - - + +
619I LEU 2.9 8.0 + - - +
620I SER* 3.5 17.7 + - - +
621I PHE 3.2 0.2 - - - -
622I VAL* 1.3 73.2 - - - +
624I ASP* 1.3 66.6 + - - +
625I LEU 2.8 8.2 + - - -
626I ASN* 2.6 32.2 - - - +
627I GLN* 5.7 0.3 - - - +
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Residues in contact with ASP 624 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620I SER* 2.9 33.3 + - - +
621I PHE* 3.3 9.8 + - - +
623I ARG* 1.3 85.9 + - - +
625I LEU* 1.3 57.1 + - - +
626I ASN 3.7 0.2 - - - -
627I GLN* 3.8 12.4 - - - +
628I TYR* 3.8 20.4 - - - -
713I LEU* 3.5 30.1 - - + +
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Residues in contact with LEU 625 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621I PHE* 3.2 26.8 + - + +
622I VAL* 3.2 8.9 + - - +
623I ARG 2.8 2.8 + - - -
624I ASP* 1.3 77.7 - - - +
626I ASN* 1.3 62.2 + - - -
627I GLN 3.2 2.5 - - - -
628I TYR* 3.1 17.4 + - + -
629I ARG* 3.6 9.2 + - - +
632I ILE* 5.6 1.3 - - + -
639I LEU* 3.9 24.5 - - + +
642I LEU* 3.3 34.3 - - + -
643I TYR* 5.7 0.7 - - + +
712I LEU* 4.0 6.7 - - + -
713I LEU* 3.2 27.4 - - + -
716I LEU* 3.9 22.7 - - + -
735I LEU* 5.3 4.0 - - + -
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Residues in contact with ASN 626 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G TRP* 3.2 54.2 - - + +
85G GLU* 3.8 12.0 - - + +
622I VAL* 3.3 4.5 + - - +
623I ARG* 2.6 28.3 + - - +
625I LEU* 1.3 71.6 - - - +
627I GLN* 1.3 70.5 + - - +
628I TYR 3.0 6.6 + - - -
629I ARG* 3.1 39.9 + - - +
643I TYR* 4.8 3.4 - - - +
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Residues in contact with GLN 627 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623I ARG 4.5 0.6 + - - +
624I ASP* 3.8 10.9 - - - +
625I LEU 3.2 1.0 - - - -
626I ASN* 1.3 82.9 + - - +
628I TYR* 1.3 103.2 + - + +
629I ARG 3.5 0.6 + - - -
630I ALA* 4.9 4.6 + - - +
631I ASP* 4.4 0.3 - - - +
717I LYS* 5.8 2.2 - - - +
720I LYS* 3.5 23.1 + - - +
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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