Contacts of the helix formed by residues 633 - 646 (chain E) in PDB entry 5U8T
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 ARG 633 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575E ASN 5.4 0.2 - - - -
576E THR* 2.9 24.6 + - - -
577E ASP* 2.5 52.1 + - - +
578E THR* 4.5 0.7 - - - +
619E LYS* 3.4 53.2 + - + +
621E ARG* 4.2 21.7 - - - +
632E ILE* 1.3 79.3 - - - +
634E ARG* 1.3 52.5 + - - +
635E GLU* 2.9 42.8 + - - +
636E ASP 3.0 5.3 + - - +
637E LEU* 2.6 35.7 + - - +
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Residues in contact with ARG 634 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577E ASP* 3.2 36.2 + - - +
579E TYR* 2.9 41.9 + - + -
633E ARG* 1.3 72.0 - - - +
635E GLU* 1.3 75.3 + - + +
637E LEU* 3.4 21.2 + - + +
638E SER* 3.6 13.7 + - - -
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Residues in contact with GLU 635 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619E LYS* 4.0 16.6 + - - +
633E ARG* 2.9 41.1 + - + +
634E ARG* 1.3 87.9 - - + +
636E ASP* 1.3 67.7 + - - +
638E SER* 4.9 0.5 - - - -
639E PRO* 3.2 17.7 - - - +
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Residues in contact with ASP 636 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618E ALA* 3.1 42.6 - - + +
619E LYS* 3.2 21.4 - - + +
632E ILE* 4.7 2.2 - - + -
633E ARG* 3.0 5.5 + - - +
635E GLU* 1.3 84.6 - - - +
637E LEU* 1.3 54.0 + - - +
638E SER 3.4 1.3 - - - -
639E PRO* 3.3 13.5 - - + +
640E PHE* 2.6 35.3 + - - +
643E LYS* 5.6 4.3 + - - +
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Residues in contact with LEU 637 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529E VAL* 5.5 8.7 - - + -
570E ALA* 5.3 3.8 - - + -
579E TYR* 3.0 54.5 - - + -
581E VAL* 5.2 2.0 - - + -
632E ILE* 3.4 20.0 - - + -
633E ARG 2.6 14.3 + - - +
634E ARG* 3.4 17.3 + - + +
636E ASP* 1.3 71.7 - - - +
638E SER* 1.3 61.4 + - - +
640E PHE* 3.1 11.5 - - + +
641E LEU* 2.6 59.7 + - + +
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Residues in contact with SER 638 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634E ARG 3.6 8.8 + - - -
635E GLU 4.9 0.7 - - - -
637E LEU* 1.3 87.6 - - - +
639E PRO* 1.4 65.5 - - - +
641E LEU* 3.0 24.5 + - - +
642E GLU* 3.0 21.3 + - - +
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Residues in contact with PRO 639 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635E GLU 3.2 18.2 - - - +
636E ASP* 3.3 26.9 - - + +
638E SER* 1.4 90.3 - - - +
640E PHE* 1.3 58.7 + - - -
642E GLU* 3.1 18.8 + - - +
643E LYS* 2.9 55.3 + - - +
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Residues in contact with PHE 640 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581E VAL* 5.3 11.7 - - + -
609E PHE* 4.0 17.5 - + - -
612E ILE* 3.4 46.7 - - + +
620E VAL* 4.1 6.3 - - + -
630E ILE* 3.6 32.1 - - + -
632E ILE* 3.7 24.5 - - + -
636E ASP 2.6 24.3 + - - +
637E LEU* 3.0 15.7 + - + +
639E PRO* 1.3 72.7 - - - +
641E LEU* 1.3 67.0 + - + +
643E LYS* 3.7 8.9 - - - +
644E LEU* 2.9 40.5 + - + +
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Residues in contact with LEU 641 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E TYR* 4.2 2.1 + - - +
527E LEU* 4.2 26.2 - - + -
529E VAL* 5.8 8.5 - - + -
568E VAL* 5.9 2.2 - - + -
637E LEU* 2.6 43.1 + - + +
638E SER* 3.0 14.8 + - - +
640E PHE* 1.3 82.9 - - + +
642E GLU* 1.3 57.4 + - - +
643E LYS 3.2 0.2 - - - -
644E LEU* 3.1 26.1 + - + +
645E THR* 2.9 34.0 + - + +
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Residues in contact with GLU 642 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638E SER* 3.0 19.5 + - - +
639E PRO* 3.1 21.3 + - - +
641E LEU* 1.3 77.2 - - + +
643E LYS* 1.3 61.8 + - + +
645E THR* 2.2 30.9 + - + +
646E LEU* 3.4 12.0 + - - +
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Residues in contact with LYS 643 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612E ILE* 4.1 12.9 - - + +
615E GLU* 3.1 43.6 - - - +
616E THR* 2.6 39.5 + - - +
618E ALA* 6.2 0.2 - - - +
636E ASP* 5.6 4.6 + - - +
639E PRO* 2.9 38.4 + - - +
640E PHE* 3.7 8.5 - - - +
642E GLU* 1.3 76.1 - - + +
644E LEU* 1.3 58.7 + - - +
646E LEU* 2.8 25.9 - - - +
647E SER 4.0 2.6 + - - +
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Residues in contact with LEU 644 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E TYR* 3.5 28.4 + - + +
527E LEU* 4.0 12.8 - - + -
568E VAL* 4.8 6.7 - - + -
605E PHE* 4.8 10.1 - - + -
608E ALA* 5.1 7.2 - - + -
609E PHE* 3.8 26.5 - - + -
612E ILE* 3.6 19.7 - - + -
640E PHE* 2.9 26.0 + - + +
641E LEU* 3.1 31.1 + - + +
643E LYS* 1.3 78.6 - - - +
645E THR* 1.3 64.3 + - - +
646E LEU* 4.5 0.4 - - - -
647E SER 4.3 7.1 - - - +
648E GLY* 4.7 2.8 - - - -
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Residues in contact with THR 645 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522E LEU* 5.7 7.2 - - + -
523E ARG* 4.7 19.2 + - - +
524E ILE* 3.9 11.3 - - - +
525E TYR* 4.0 17.0 - - + +
641E LEU* 2.9 20.0 + - + +
642E GLU* 2.2 33.2 + - - +
644E LEU* 1.3 78.9 - - - +
646E LEU* 1.3 68.2 + - - +
648E GLY* 3.2 18.1 + - - -
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Residues in contact with LEU 646 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523E ARG* 6.1 3.1 - - - +
615E GLU* 4.9 3.6 - - - +
642E GLU 4.0 4.9 - - - +
643E LYS* 2.8 28.7 - - - +
645E THR* 1.3 91.4 + - - +
647E SER* 1.3 58.4 + - - +
648E GLY 3.5 0.9 - - - +
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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