Contacts of the helix formed by residues 602 - 618 (chain B) in PDB entry 2EYQ
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 THR 602 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459B GLN* 6.1 4.9 - - + -
600B GLU 4.2 0.4 + - - -
601B THR* 1.3 73.5 - - - +
603B PRO* 1.3 71.5 - - + +
604B ASP* 3.6 22.2 - - + +
605B GLN* 2.6 30.3 + - - +
606B ALA* 2.7 34.7 + - - +
634B LYS* 4.2 11.4 + - - +
776B ILE* 5.3 4.0 - - + -
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Residues in contact with PRO 603 (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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601B THR 4.3 2.5 - - - +
602B THR* 1.3 93.6 - - + +
604B ASP* 1.3 56.6 + - - +
606B ALA* 3.2 5.8 + - + +
607B GLN* 2.7 52.5 + - - +
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Residues in contact with ASP 604 (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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602B THR* 3.6 13.7 - - + +
603B PRO* 1.3 79.6 - - - +
605B GLN* 1.3 53.7 + - - +
607B GLN* 3.5 12.9 + - - +
608B ALA* 2.8 35.7 + - - +
775B ILE 3.6 24.6 - - - +
776B ILE* 4.0 13.3 - - + +
777B ALA* 4.6 19.6 + - - +
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Residues in contact with GLN 605 (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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597B PHE* 5.7 1.8 - - - -
600B GLU 4.3 2.3 - - - +
601B THR* 3.2 15.7 - - + +
602B THR* 2.6 46.1 + - - +
604B ASP* 1.3 80.2 - - - +
606B ALA* 1.3 63.1 + - - +
608B ALA* 3.3 2.4 + - - +
609B ILE* 3.1 33.5 + - + +
632B PHE 3.4 9.9 + - - +
633B GLY* 3.4 24.0 - - - +
634B LYS* 2.8 47.9 - - + +
636B GLU* 5.9 0.4 - - + -
637B VAL* 4.3 3.8 - - + +
776B ILE* 3.9 15.6 - - + +
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Residues in contact with ALA 606 (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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601B THR* 3.4 21.0 + - - +
602B THR 2.7 16.0 + - - +
603B PRO* 3.7 5.4 - - + +
605B GLN* 1.3 73.1 - - - +
607B GLN* 1.3 58.3 + - + +
609B ILE* 3.3 10.6 + - + +
610B ASN* 2.8 42.6 + - - +
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Residues in contact with GLN 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B PRO* 2.7 38.0 + - - +
604B ASP* 3.2 12.4 + - - +
606B ALA* 1.3 75.1 - - + +
608B ALA* 1.3 56.5 + - - +
610B ASN* 3.9 8.0 - - - +
611B ALA* 3.0 26.5 + - - +
774B SER* 4.7 1.0 + - - -
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Residues in contact with ALA 608 (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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604B ASP 2.8 20.1 + - - +
605B GLN 3.8 4.0 - - - +
607B GLN* 1.3 70.2 - - - +
609B ILE* 1.3 61.2 + - - +
611B ALA* 3.1 1.9 + - - +
612B VAL* 2.8 36.8 + - - +
626B VAL* 4.1 19.1 - - + -
637B VAL* 4.1 8.7 - - + -
774B SER* 3.7 30.5 - - - -
775B ILE 5.6 0.4 - - - +
776B ILE* 4.6 5.8 - - + -
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Residues in contact with ILE 609 (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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590B TYR* 3.9 5.6 - - - +
601B THR* 4.8 8.7 - - + -
605B GLN* 3.1 19.9 + - + +
606B ALA* 3.4 13.5 - - - +
608B ALA* 1.3 77.4 - - - +
610B ASN* 1.3 70.2 + - - +
612B VAL* 3.1 4.3 + - - +
613B LEU* 2.8 45.0 + - + +
636B GLU* 4.6 13.2 - - + -
637B VAL* 3.6 24.9 - - + +
640B ARG* 3.6 44.2 - - + +
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Residues in contact with ASN 610 (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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590B TYR* 5.0 5.0 + - - -
606B ALA* 2.8 32.0 + - - +
607B GLN* 3.9 7.3 - - - +
609B ILE* 1.3 80.6 - - - +
611B ALA* 1.3 53.1 - - - +
613B LEU* 3.2 8.4 + - - +
614B SER* 2.8 36.4 + - - -
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Residues in contact with ALA 611 (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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607B GLN 3.0 16.0 + - - +
608B ALA 3.1 8.5 + - - +
610B ASN* 1.3 76.1 - - - +
612B VAL* 1.3 63.1 + - - +
614B SER* 3.0 22.3 + - - -
615B ASP* 3.1 13.7 + - - -
624B ARG* 3.8 16.6 - - - +
774B SER* 3.4 20.2 - - - +
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Residues in contact with VAL 612 (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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608B ALA 2.8 25.4 + - - +
609B ILE* 3.7 4.9 - - - +
611B ALA* 1.3 71.9 - - - +
613B LEU* 1.3 65.0 + - + +
616B MET* 3.1 26.2 + - + +
622B MET* 3.1 25.0 - - + +
624B ARG* 3.9 15.7 - - - -
626B VAL* 4.4 4.5 - - + -
637B VAL* 4.1 17.5 - - + +
641B ALA* 4.0 27.4 - - + -
752B LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 613 (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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585B HIS* 4.7 15.0 - - + +
590B TYR* 3.7 29.6 - - + +
609B ILE* 2.8 40.1 + - + +
610B ASN* 3.6 9.4 - - - +
612B VAL* 1.3 76.1 - - + +
614B SER* 1.3 68.6 + - - +
616B MET* 3.3 6.0 + - - +
617B CYS* 3.1 25.4 + - - -
640B ARG* 4.6 12.6 - - + +
641B ALA* 4.7 8.1 - - - +
644B LEU* 3.8 34.1 - - + -
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Residues in contact with SER 614 (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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610B ASN 2.8 17.3 + - - -
611B ALA* 3.0 12.5 + - - -
613B LEU* 1.3 71.2 - - - +
615B ASP* 1.3 83.6 + - - +
617B CYS* 2.8 24.9 + - - +
618B GLN* 3.1 17.0 + - - +
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Residues in contact with ASP 615 (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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611B ALA 3.1 8.5 + - - +
614B SER* 1.3 87.8 + - - +
616B MET* 1.3 66.1 + - - +
618B GLN* 2.9 33.3 + - - +
620B LEU 4.0 7.1 - - - +
622B MET* 3.3 32.5 - - + +
624B ARG* 2.7 41.3 + - - +
750B ASP* 4.7 0.2 - - - +
772B ASP* 4.7 5.9 - - - +
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Residues in contact with MET 616 (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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581B PHE 3.8 2.1 - - - +
583B PHE* 3.0 62.2 + - + -
612B VAL* 3.1 23.6 + - - +
613B LEU* 3.5 7.0 - - - +
614B SER 3.2 0.2 - - - -
615B ASP* 1.3 78.9 - - - +
617B CYS* 1.3 57.5 + - - +
618B GLN 3.4 5.5 + - - +
622B MET* 3.7 17.3 - - - +
641B ALA* 3.8 34.8 - - - +
644B LEU* 3.6 22.4 - - + -
645B ALA* 4.3 2.2 - - + -
725B LEU* 3.6 30.5 - - + -
750B ASP* 4.1 11.7 - - + +
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Residues in contact with CYS 617 (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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582B ALA* 3.3 19.2 - - - +
583B PHE 3.3 25.0 - - - +
585B HIS* 3.9 28.9 - - - -
613B LEU* 3.1 17.0 + - - +
614B SER* 2.8 21.3 + - - +
616B MET* 1.3 70.0 - - - +
618B GLN* 1.3 59.4 + - + -
619B PRO* 4.3 0.7 - - - +
644B LEU* 4.6 7.0 - - - -
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Residues in contact with GLN 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B PHE 3.7 5.5 - - - +
582B ALA* 4.0 1.6 - - - -
614B SER* 3.4 19.6 + - - +
615B ASP* 2.9 21.2 + - - +
616B MET 3.6 5.7 - - - +
617B CYS* 1.3 81.8 - - + +
619B PRO* 1.3 69.7 - - + +
620B LEU* 3.0 37.2 + - + +
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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