Contacts of the helix formed by residues 583 - 591 (chain C) in PDB entry 5D4D
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 LEU 583 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.7 29.8 - - + -
18C LEU* 6.0 0.9 - - + -
457C ALA* 5.2 2.0 - - + -
537C LYS* 3.8 37.7 - - + +
542C VAL* 4.2 22.4 - - + +
545C ASN* 3.5 34.8 - - + +
546C LEU* 3.8 16.2 - - + -
581C THR* 3.5 5.6 + - - +
582C GLY* 1.3 78.6 - - - +
584C GLU* 1.3 64.9 + - - +
585C GLU 3.1 4.4 + - - -
586C ARG* 3.3 8.3 + - + +
587C VAL* 3.2 26.0 + - + +
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Residues in contact with GLU 584 (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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546C LEU* 3.7 19.2 - - + +
577C PRO* 4.4 5.6 - - + -
580C MET* 3.3 39.6 - - + +
581C THR* 2.8 26.2 + - - -
582C GLY* 2.7 24.7 + - - -
583C LEU* 1.3 72.8 - - - +
585C GLU* 1.3 58.7 + - - +
587C VAL* 3.9 0.6 + - - +
588C VAL* 3.2 13.9 + - - +
665C PHE* 4.3 5.3 - - + -
666C LEU* 3.0 52.3 + - + +
842C ARG* 4.4 7.8 + - - -
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Residues in contact with GLU 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 5.9 0.9 + - - -
582C GLY 4.6 6.4 + - - +
583C LEU 3.2 0.4 - - - -
584C GLU* 1.3 75.2 - - - +
586C ARG* 1.3 66.1 + - + +
587C VAL 3.1 1.6 - - - -
588C VAL* 3.2 4.9 + - - +
589C ARG* 3.0 23.6 + - - +
596C TYR* 4.4 1.6 + - - -
664C GLY 3.5 17.9 - - - +
665C PHE* 3.1 48.9 - - + -
902C ILE* 5.3 5.9 - - - +
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Residues in contact with ARG 586 (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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14C PRO* 4.3 8.1 - - - +
15C LEU* 2.6 63.2 + - + +
16C PRO 3.0 13.9 + - - -
17C PRO* 3.9 2.4 - - - +
18C LEU* 4.2 7.2 - - + +
582C GLY 5.2 2.6 + - - +
583C LEU* 3.3 14.3 + - + +
585C GLU* 1.3 78.3 - - + +
587C VAL* 1.3 58.2 + - + +
589C ARG* 3.3 14.0 + - - +
590C ASP* 2.9 76.1 + - - +
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Residues in contact with VAL 587 (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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18C LEU* 4.9 3.8 - - + -
400C PRO* 5.9 0.2 - - + -
401C LEU* 4.3 14.6 - - + +
404C LEU* 4.0 19.8 - - + +
542C VAL* 3.9 26.9 - - + -
546C LEU* 4.5 11.7 - - + -
583C LEU* 3.2 24.3 + - + +
584C GLU 4.0 5.2 - - - +
585C GLU 3.1 0.6 - - - -
586C ARG* 1.3 74.2 - - + +
588C VAL* 1.3 65.7 + - - +
590C ASP* 4.3 0.2 - - - +
591C SER* 2.9 31.8 + - - +
666C LEU* 3.9 27.6 - - + -
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Residues in contact with VAL 588 (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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400C PRO* 6.0 0.7 - - - -
584C GLU 3.2 18.2 - - - +
585C GLU 3.2 1.9 + - - +
587C VAL* 1.3 75.5 - - - +
589C ARG* 1.3 63.2 + - - +
591C SER* 3.3 16.2 + - - -
592C LEU* 4.1 0.2 - - - -
593C ALA* 3.4 15.5 + - + -
594C ALA* 3.6 32.5 + - + +
596C TYR* 3.8 5.0 + - - +
661C SER* 3.6 20.0 - - - +
664C GLY 3.5 16.4 - - - +
665C PHE 3.5 2.9 - - - +
666C LEU* 3.3 32.1 - - + +
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Residues in contact with ARG 589 (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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585C GLU 3.0 16.5 + - - +
586C ARG* 3.7 16.6 - - - +
588C VAL* 1.3 78.6 - - - +
590C ASP* 1.3 69.1 + - - +
592C LEU* 3.2 19.2 + - - +
596C TYR* 3.3 54.7 + - + +
652C GLY* 2.6 36.1 + - - -
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Residues in contact with ASP 590 (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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17C PRO* 3.7 3.6 - - - +
18C LEU* 2.8 47.4 + - + +
19C THR* 4.2 16.9 + - - +
124C ASP* 5.5 2.1 - - - +
404C LEU* 4.6 3.8 - - + -
586C ARG* 2.9 51.4 + - - +
587C VAL 4.3 1.1 - - - +
589C ARG* 1.3 75.8 - - - +
591C SER* 1.3 60.3 + - - +
592C LEU* 3.0 15.2 + - - +
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Residues in contact with SER 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 5.7 0.7 - - - -
124C ASP* 4.6 9.0 - - - +
400C PRO* 3.4 30.4 - - - +
403C SER* 6.1 1.4 - - - -
404C LEU* 4.6 14.5 - - - +
407C LYS* 5.5 3.7 + - - +
587C VAL* 2.9 22.0 + - - -
588C VAL* 3.3 3.3 + - - -
590C ASP* 1.3 74.4 - - - +
592C LEU* 1.3 69.1 + - - +
593C ALA* 3.1 25.5 + - - +
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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