Contacts of the helix formed by residues 650 - 670 (chain A) in PDB entry 4D2Y
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 ASP 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A MET* 4.1 0.9 - - - -
590A GLY* 4.6 1.1 - - - +
638A LEU* 3.6 33.4 - - + +
649A VAL* 1.3 76.7 - - - +
651A HIS* 1.3 65.0 + - - +
652A HIS* 2.9 20.3 + - - +
653A SER* 2.8 33.9 + - - -
654A ALA* 3.0 22.3 + - - +
621B THR* 3.2 18.5 + - - -
622B SER* 3.6 20.6 - - - -
624B LEU* 4.5 5.4 - - + -
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Residues in contact with HIS 651 (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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589A MET* 3.7 18.4 - - - +
590A GLY* 5.1 0.6 - - - +
591A THR* 3.5 22.7 + - + +
634A ASN* 5.7 0.4 - - + -
638A LEU* 5.5 1.2 - - - +
649A VAL 4.0 0.4 + - - -
650A ASP* 1.3 73.8 - - - +
652A HIS* 1.3 76.5 + + - +
655A THR* 2.8 34.7 + - - +
681A PRO* 3.8 22.7 - - + -
683A MET* 3.9 28.5 - - + +
684A SER* 4.1 2.8 - - - -
688A THR* 4.0 12.7 - - + +
624B LEU* 3.6 27.5 - - + +
627B ASP* 2.8 28.7 + - - -
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Residues in contact with HIS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ASP* 2.9 11.7 + - - +
651A HIS* 1.3 96.5 + + - +
653A SER* 1.3 63.7 + - - +
655A THR* 3.3 5.5 + - - -
656A GLU* 3.0 27.2 + - - +
687A ILE* 3.6 39.8 + - + -
688A THR* 3.9 10.5 - - + +
689A PRO* 4.9 3.2 - - - +
621B THR* 3.9 25.8 - - + -
624B LEU* 3.8 14.8 - - + -
626B LYS* 4.3 16.1 + - + +
627B ASP* 2.7 26.1 + - - -
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Residues in contact with SER 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A VAL* 3.6 20.8 - - - +
650A ASP* 2.8 24.6 + - - -
652A HIS* 1.3 72.1 - - - +
654A ALA* 1.3 58.2 + - - +
656A GLU* 3.3 14.6 + - - +
657A SER* 2.8 38.1 + - - -
860A ACT 4.8 0.7 + - - -
621B THR* 4.5 4.9 + - - -
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Residues in contact with ALA 654 (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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416A VAL* 4.0 16.7 - - + +
589A MET* 3.6 25.4 - - - -
649A VAL* 3.6 16.7 - - + +
650A ASP 3.0 17.7 + - - +
653A SER* 1.3 78.1 + - - +
655A THR* 1.3 57.0 + - - +
657A SER* 3.3 4.5 + - - -
658A PHE* 3.0 25.8 + - - +
750A HEM 5.5 0.2 - - + -
860A ACT 3.8 15.7 - - + +
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Residues in contact with THR 655 (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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416A VAL* 4.4 7.0 - - + -
589A MET* 5.1 0.9 - - - -
651A HIS* 2.8 24.2 + - - +
652A HIS 3.3 5.0 + - - -
654A ALA* 1.3 74.5 - - + +
656A GLU* 1.3 67.9 + - - +
658A PHE* 3.1 5.8 + - - +
659A ILE* 3.0 27.9 + - - +
679A ILE 4.3 4.9 - - - +
681A PRO* 3.5 26.9 - - + -
688A THR* 3.5 16.2 - - - -
689A PRO* 3.5 6.7 - - - +
690A VAL* 3.7 31.3 - - + +
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Residues in contact with GLU 656 (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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652A HIS 3.0 21.2 + - - +
653A SER* 3.5 11.1 + - - +
655A THR* 1.3 78.8 + - - +
657A SER* 1.3 63.3 + - - +
659A ILE* 3.4 5.5 + - - +
660A LYS* 3.3 19.1 + - - +
689A PRO* 3.9 15.2 - - + +
621B THR* 6.0 2.3 - - - +
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Residues in contact with SER 657 (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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416A VAL 5.8 0.4 - - - -
419A ILE* 3.6 24.5 - - - +
653A SER* 2.8 20.3 + - - -
654A ALA 3.4 9.4 - - - -
655A THR 3.2 0.2 - - - -
656A GLU* 1.3 78.4 - - - +
658A PHE* 1.3 57.8 - - - +
660A LYS* 3.3 9.1 - - - +
661A HIS* 3.0 26.4 - - - -
860A ACT 3.4 20.2 + - - -
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Residues in contact with PHE 658 (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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415A CYS 3.8 8.3 - - - -
416A VAL* 3.5 33.4 + - + +
418A ARG* 3.3 36.8 - - - -
419A ILE* 5.5 1.3 - - - -
654A ALA 3.0 17.0 + - - +
655A THR* 3.1 6.0 + - - +
657A SER* 1.3 74.9 + - - +
659A ILE* 1.3 59.3 + - - +
661A HIS* 3.2 21.4 + + - +
662A MET* 2.8 56.3 + - + +
672A CYS* 4.4 2.0 - - - -
674A ALA* 3.8 12.6 - - + -
679A ILE* 3.8 26.9 - - + -
690A VAL* 4.0 9.9 - - + -
695A MET* 4.2 5.6 - - + -
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Residues in contact with ILE 659 (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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305A ASN* 4.7 4.7 - - - +
655A THR 3.0 17.8 + - - +
656A GLU* 3.7 8.5 - - - +
657A SER 3.3 0.2 - - - +
658A PHE* 1.3 75.3 - - - +
660A LYS* 1.3 62.5 + - - +
662A MET* 3.1 10.3 + - + +
663A GLU* 3.0 43.6 + - + +
689A PRO* 3.7 25.4 - - + -
690A VAL* 3.7 20.9 - - + +
693A GLN* 3.8 39.7 - - + +
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Residues in contact with LYS 660 (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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419A ILE* 4.3 13.4 - - + +
656A GLU 3.3 11.0 + - - +
657A SER* 3.5 10.5 - - - +
658A PHE 3.2 0.4 - - - -
659A ILE* 1.3 79.8 - - - +
661A HIS* 1.3 56.3 + - - +
663A GLU* 3.3 14.1 + - - +
664A ASN* 2.9 50.2 + - - +
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Residues in contact with HIS 661 (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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410A ARG* 5.0 2.2 + - + -
418A ARG* 3.3 42.2 - - + +
419A ILE* 3.6 25.7 + - + +
421A TRP* 3.6 14.3 - + - -
657A SER 3.0 14.7 - - - -
658A PHE* 3.2 26.7 + + - +
660A LYS* 1.3 74.3 - - - +
662A MET* 1.3 66.5 + - - +
664A ASN* 3.1 13.0 + - - +
665A GLU* 2.8 63.1 + - + +
672A CYS* 4.2 9.5 - - - -
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Residues in contact with MET 662 (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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303A VAL* 4.8 0.4 - - + -
312A LEU* 4.7 4.9 - - + -
658A PHE* 2.8 51.9 + - + +
659A ILE* 3.4 12.6 - - + +
661A HIS* 1.3 75.1 - - - +
663A GLU* 1.3 59.8 + - + +
665A GLU* 3.5 4.3 - - - +
666A TYR* 2.8 65.1 + - + +
672A CYS* 4.2 16.2 - - - +
674A ALA* 5.0 1.1 - - + -
693A GLN* 3.7 41.3 - - + +
694A GLU 4.1 7.2 - - - +
695A MET* 4.2 11.9 - - + -
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Residues in contact with GLU 663 (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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310A VAL* 4.6 17.5 - - + +
312A LEU* 4.4 25.8 - - + +
659A ILE* 3.0 32.8 + - + +
660A LYS* 3.7 13.4 - - - +
662A MET* 1.3 75.5 - - + +
664A ASN* 1.3 64.5 + - - +
666A TYR* 3.6 2.0 + - - +
667A ARG* 3.1 27.3 + - - +
693A GLN* 5.6 0.7 - - - +
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Residues in contact with ASN 664 (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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419A ILE* 4.7 8.3 - - - +
660A LYS* 2.9 43.8 + - - +
661A HIS* 3.1 13.2 + - - +
663A GLU* 1.3 76.9 - - - +
665A GLU* 1.3 57.7 + - + +
667A ARG* 2.9 31.1 + - - +
668A CYS* 2.8 41.9 + - - +
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Residues in contact with GLU 665 (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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410A ARG* 2.7 56.3 + - - +
421A TRP* 4.4 3.2 + - - -
661A HIS* 2.8 52.3 + - + +
662A MET 3.5 4.3 - - - +
664A ASN* 1.3 75.7 - - - +
666A TYR* 1.3 57.9 + - - +
668A CYS* 5.2 2.1 - - - +
669A ARG* 2.7 41.1 + - - +
670A GLY 3.1 5.2 + - - -
671A GLY 3.4 17.1 + - - +
672A CYS* 3.6 11.7 - - + -
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Residues in contact with TYR 666 (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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303A VAL* 3.6 24.9 - - + +
312A LEU* 3.5 41.1 - - + -
313A THR 3.3 25.0 - - - +
314A ASP* 3.0 43.7 + - + +
662A MET* 2.8 54.8 + - + +
663A GLU 4.0 2.9 - - - +
665A GLU* 1.3 73.1 - - - +
667A ARG* 1.3 63.2 + - - +
670A GLY* 3.3 17.5 + - - -
671A GLY* 3.6 10.5 - - - +
672A CYS* 3.5 21.8 + - + -
696A LEU* 4.4 5.7 + - - +
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Residues in contact with ARG 667 (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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663A GLU* 3.1 19.0 + - - +
664A ASN* 2.9 35.2 + - - +
666A TYR* 1.3 79.7 - - - +
668A CYS* 1.3 79.1 + - - +
669A ARG 3.6 0.4 + - - -
670A GLY 4.9 0.5 + - - -
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Residues in contact with CYS 668 (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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410A ARG* 5.1 6.1 - - - +
664A ASN* 2.8 24.7 + - - +
665A GLU* 5.2 3.8 - - - +
667A ARG* 1.3 103.8 - - - +
669A ARG* 1.3 60.9 - - + +
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Residues in contact with ARG 669 (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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315A THR* 4.9 0.3 + - - -
316A LEU* 3.6 47.0 - - + +
319A LYS* 5.8 1.0 - - - -
364A GLN* 5.3 5.1 - - - +
407A HIS* 4.0 15.1 - - - -
410A ARG* 3.7 52.7 + - - +
411A ASN* 2.8 38.2 + - - +
665A GLU* 2.7 26.0 + - - +
667A ARG 3.6 0.2 - - - -
668A CYS* 1.3 76.3 + - - +
670A GLY* 1.3 61.2 + - - +
671A GLY 3.5 4.6 + - - +
672A CYS* 5.8 0.2 - - - +
673A PRO* 4.6 4.9 - - - +
700A LEU* 4.1 8.1 - - - +
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Residues in contact with GLY 670 (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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313A THR 4.2 5.4 - - - -
314A ASP* 3.3 5.4 - - - -
315A THR* 2.8 43.0 + - - -
316A LEU* 3.2 6.3 + - - -
665A GLU 3.1 2.6 + - - -
666A TYR* 3.3 16.8 + - - -
667A ARG 4.7 0.4 + - - -
669A ARG* 1.3 78.4 - - - +
671A GLY* 1.3 56.7 + - - +
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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