Contacts of the helix formed by residues 601 - 613 (chain C) in PDB entry 5UH8
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 601 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600C ASP* 1.3 74.8 - - - +
602C ALA* 1.3 76.9 + - - +
603C ASN* 2.7 33.0 + - + +
604C ARG* 3.3 3.7 + - - +
605C ALA* 2.9 19.4 + - - +
925C ARG 4.2 6.9 + - - +
926C MET* 3.2 34.9 + - + +
927C ASN* 5.2 0.2 - - - +
816D THR* 5.4 0.7 - - - +
821D LYS* 3.9 15.9 + - - -
840D PHE* 3.4 27.4 - - + -
852D ASN* 4.0 7.6 + - - +
856D ALA* 4.5 2.1 - - - +
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Residues in contact with ALA 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C ILE* 4.3 5.7 - - + +
600C ASP 3.7 0.6 + - - -
601C ASP* 1.3 77.8 + - - +
603C ASN* 1.3 58.4 + - - +
605C ALA* 3.8 6.9 - - - +
606C LEU* 2.8 33.2 + - + +
849D TYR* 4.1 7.7 + - + -
852D ASN* 4.5 5.4 - - - +
853D THR* 3.8 33.0 - - + +
856D ALA* 3.7 25.4 - - + -
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Residues in contact with ASN 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C ASP* 2.7 30.7 + - + +
602C ALA* 1.3 79.9 - - - +
604C ARG* 1.3 71.3 + - + +
606C LEU* 3.5 15.8 - - - +
607C MET* 3.5 18.6 - - + +
856D ALA* 3.7 19.6 - - - +
860D LEU* 3.3 42.1 - - + +
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Residues in contact with ARG 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C ASP* 3.3 5.1 + - + +
603C ASN* 1.3 80.8 - - + +
605C ALA* 1.3 60.3 + - - +
606C LEU 3.2 2.2 - - - -
607C MET* 3.4 24.4 + - - +
608C GLY 3.0 21.5 + - - -
733C ASP* 5.2 5.5 + - - -
889C HIS 3.5 15.7 - - - +
890C GLY* 3.2 36.5 + - - -
891C ASN* 4.7 4.4 - - - +
892C LYS* 4.2 18.7 - - - +
925C ARG* 3.1 85.0 - - + +
927C ASN* 3.8 9.3 - - + +
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Residues in contact with ALA 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C ILE* 3.8 12.2 - - + +
594C ILE* 3.7 10.5 - - - +
597C LEU* 3.7 18.8 - - + -
600C ASP* 4.3 9.0 - - + +
601C ASP 2.9 17.6 + - - +
602C ALA* 3.8 4.9 - - - +
604C ARG* 1.3 76.5 - - - +
606C LEU* 1.3 63.4 + - - +
608C GLY* 3.2 3.7 + - - +
609C ALA 3.2 17.0 + - - -
888C ARG 5.4 0.4 - - - -
889C HIS* 5.2 3.1 - - - +
849D TYR* 3.5 20.4 - - - +
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Residues in contact with LEU 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C PRO 5.6 0.2 - - - +
486C ILE* 3.4 33.3 - - + +
487C GLU* 5.6 0.3 - - - -
488C THR* 3.3 35.2 - - + +
489C PRO 4.6 2.7 - - - +
490C GLU* 3.6 25.1 - - + -
494C ILE* 5.5 3.8 - - + -
602C ALA* 2.8 19.7 + - + +
603C ASN* 3.5 8.1 - - - +
604C ARG 3.2 0.2 - - - -
605C ALA* 1.3 76.9 - - - +
607C MET* 1.3 63.0 + - - +
609C ALA* 3.2 6.8 + - - +
610C ASN* 3.1 30.0 + - - +
857D ARG* 5.2 6.3 - - + +
860D LEU* 4.6 19.7 - - + -
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Residues in contact with MET 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C GLU* 3.2 38.8 - - + +
603C ASN* 3.5 20.4 - - + +
604C ARG* 3.4 33.6 + - - +
605C ALA 3.4 0.2 - - - -
606C LEU* 1.3 77.3 - - + +
608C GLY* 1.3 56.2 - - - +
610C ASN* 4.3 6.7 - - - -
611C MET* 2.8 48.5 + - + +
890C GLY* 4.1 8.3 - - - +
892C LYS* 3.3 36.3 - - - +
860D LEU* 6.4 1.8 - - + -
4I A 5.2 0.2 - - - -
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Residues in contact with GLY 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C ILE* 3.9 0.9 - - - -
604C ARG 3.0 11.2 + - - -
605C ALA 3.5 4.7 - - - -
606C LEU 3.1 0.8 - - - -
607C MET* 1.3 77.4 - - - +
609C ALA* 1.3 58.4 + - - +
611C MET* 3.7 4.5 + - - +
612C GLN* 2.9 31.6 + - - +
887C GLY 4.8 0.5 - - - +
888C ARG* 3.3 26.6 - - - +
890C GLY* 3.6 12.0 - - - -
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Residues in contact with ALA 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C ILE* 4.8 2.9 - - + -
487C GLU* 4.1 30.6 - - + +
590C ALA* 4.4 12.4 - - - +
591C THR* 4.5 7.9 - - - +
594C ILE* 3.7 8.4 - - + +
605C ALA 3.2 11.1 + - - +
606C LEU 3.7 6.7 - - - +
608C GLY* 1.3 74.1 - - - +
610C ASN* 1.3 67.9 + - - +
611C MET 3.2 1.0 + - - -
612C GLN* 3.3 24.7 + - - +
613C ARG* 3.7 10.9 - - - +
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Residues in contact with ASN 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C GLU* 4.4 1.9 - - - +
488C THR 2.8 39.9 + - - +
489C PRO* 3.6 10.6 - - - +
490C GLU* 4.1 5.4 - - - +
606C LEU* 3.1 24.5 + - - +
607C MET* 3.8 6.5 - - - +
609C ALA* 1.3 80.3 - - - +
611C MET* 1.3 62.3 + - + +
613C ARG* 2.9 45.4 + - - +
614C GLN* 3.5 18.6 + - - +
2I C 5.6 1.1 - - - +
3I G 4.2 15.9 + - - +
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Residues in contact with MET 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607C MET* 2.8 23.2 + - + +
608C GLY* 4.3 2.0 - - - +
610C ASN* 1.3 76.2 - - - +
612C GLN* 1.3 57.4 + - - +
613C ARG 3.1 2.2 - - - -
614C GLN* 2.7 40.9 + - - +
615C ALA 3.4 0.2 + - - -
884C LYS* 4.5 5.8 - - - +
886C ALA* 3.7 17.9 - - + -
887C GLY 3.9 7.9 - - - +
890C GLY* 3.7 34.5 - - - -
892C LYS* 3.9 25.4 - - + -
1031C MET* 4.3 4.0 - - + -
1033C LEU* 3.4 39.9 - - + +
3I G 4.9 5.4 - - - +
4I A 5.1 1.6 - - - +
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Residues in contact with GLN 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C ASN* 2.8 29.8 + - - +
446C LEU* 4.0 9.6 - - + -
590C ALA 3.3 18.7 + - - +
593C MET* 3.6 40.4 + - - +
594C ILE* 3.4 12.1 - - - +
608C GLY 2.9 20.6 - - - +
609C ALA* 3.3 11.8 + - - +
611C MET* 1.3 77.0 - - - +
613C ARG* 1.3 50.7 + - - +
614C GLN 3.1 0.9 + - - -
615C ALA* 3.2 6.8 + - - +
715C LEU* 3.8 19.5 - - + +
888C ARG* 4.2 14.4 - - + +
1031C MET* 3.6 28.5 - - + -
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Residues in contact with ARG 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C ASP* 4.4 7.3 + - - +
443C ASN* 3.5 13.3 + - - +
444C ASN* 3.7 6.3 - - - +
446C LEU* 5.0 3.4 - - + -
447C SER* 3.3 37.2 + - - +
450C THR* 3.6 37.3 - - - +
454C ARG* 3.4 25.9 - - - +
487C GLU* 3.1 24.4 + - - +
488C THR* 6.1 0.2 - - - +
489C PRO* 6.1 0.4 - - - +
590C ALA* 5.0 3.6 - - + -
609C ALA 3.7 12.3 - - - +
610C ASN* 2.9 41.0 + - - +
611C MET 3.1 0.6 - - - -
612C GLN* 1.3 75.1 - - - +
614C GLN* 1.3 60.5 + - + +
615C ALA 3.5 0.7 - - - -
2I C 3.4 32.3 + - - -
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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