Contacts of the helix formed by residues 584 - 594 (chain C) in PDB entry 1V40
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 ILE 584 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424C TYR* 4.1 20.2 - - + -
540C TRP* 4.2 11.2 - - + -
546C VAL* 4.1 21.5 - - + -
551C PHE* 4.1 22.2 - - + -
580C LYS 3.4 10.5 + - - +
581C VAL* 3.1 24.9 + - - +
583C ALA* 1.3 74.0 - - - +
585C PRO* 1.3 67.7 - - + -
586C ALA* 4.1 7.2 - - + +
587C VAL* 2.8 18.6 + - + -
588C ALA* 2.7 32.7 + - - +
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Residues in contact with PRO 585 (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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583C ALA 2.9 8.9 - - - +
584C ILE* 1.3 87.0 - - + +
586C ALA* 1.3 62.5 + - - +
588C ALA* 3.3 5.3 + - + +
589C ASN* 2.9 25.7 + - - +
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Residues in contact with ALA 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ALA* 3.5 29.4 - - - +
424C TYR* 4.0 16.8 - - + +
584C ILE* 3.4 7.6 - - + +
585C PRO* 1.3 78.8 - - - +
587C VAL* 1.3 61.6 + - - +
589C ASN* 3.7 8.2 + - - +
590C TRP* 3.3 20.4 + - - +
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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
----------------------------------------------------------
420C TYR* 4.0 28.9 - - + +
423C ALA* 5.3 2.0 - - - -
424C TYR* 4.6 8.5 - - + -
551C PHE* 4.0 28.3 - - + -
581C VAL* 3.6 21.8 - - + +
584C ILE* 2.8 26.0 + - + +
586C ALA* 1.3 74.2 - - - +
588C ALA* 1.3 60.2 + - - +
589C ASN 3.1 1.6 - - - -
590C TRP* 3.1 5.7 + - - +
591C ILE* 2.9 46.9 + - + +
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Residues in contact with ALA 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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582C GLN 3.1 23.5 + - - +
583C ALA 4.5 3.6 - - - +
584C ILE 2.7 18.4 + - - +
585C PRO* 3.8 6.3 - - + +
587C VAL* 1.3 73.8 - - - +
589C ASN* 1.3 56.6 + - - +
591C ILE* 3.5 7.6 + - - +
592C LYS* 3.0 29.5 + - - +
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Residues in contact with ASN 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 PRO 2.9 16.8 + - - +
586C ALA* 3.7 9.2 + - - +
588C ALA* 1.3 75.1 - - - +
590C TRP* 1.3 66.5 + - - +
592C LYS* 3.2 10.4 + - - +
593C ARG* 3.0 57.3 + - - +
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Residues in contact with TRP 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C GLU* 2.7 27.8 + - - -
419C ARG* 3.4 31.2 - - + +
420C TYR* 3.7 26.9 - + - -
423C ALA* 3.9 20.2 - - + -
429C TYR* 3.9 11.7 - + - -
431C ASP* 3.7 22.2 - - - -
433C ARG* 3.8 8.1 - - - -
586C ALA 3.3 10.3 + - - +
587C VAL* 3.1 9.0 + - - +
589C ASN* 1.3 80.1 - - - +
591C ILE* 1.3 61.6 + - + +
593C ARG* 3.0 6.7 + - + -
594C ARG* 2.8 59.8 + - + +
595C PRO* 4.6 2.5 - - + -
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Residues in contact with ILE 591 (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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420C TYR* 3.7 28.7 - - + +
554C GLU* 4.0 3.8 - - - +
582C GLN* 4.0 29.6 - - + -
587C VAL* 2.9 36.6 + - + +
588C ALA* 3.7 7.9 - - - +
590C TRP* 1.3 76.7 - - - +
592C LYS* 1.3 61.5 + - - +
594C ARG* 3.6 39.9 + - - +
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Residues in contact with LYS 592 (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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588C ALA 3.0 17.9 + - - +
589C ASN* 3.6 8.5 - - - +
590C TRP 3.1 0.2 - - - -
591C ILE* 1.3 80.2 - - - +
593C ARG* 1.3 86.8 + - - +
594C ARG 4.5 0.2 - - - +
603D ASN* 3.3 17.5 - - - +
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Residues in contact with ARG 593 (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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589C ASN* 3.0 44.7 + - - +
590C TRP* 4.1 7.6 - - + +
592C LYS* 1.3 102.0 - - - +
594C ARG* 1.3 65.3 + - - +
595C PRO* 4.3 2.3 - - - +
603D ASN* 3.7 7.8 + - - +
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Residues in contact with ARG 594 (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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412C ARG* 3.4 31.5 - - - +
416C GLU* 2.8 29.8 + - - +
420C TYR* 3.2 25.5 + - - -
433C ARG* 4.8 1.1 - - - +
554C GLU* 5.4 1.0 + - - -
558C THR* 4.8 12.1 + - - +
590C TRP* 2.8 45.9 + - + +
591C ILE* 3.6 38.0 + - - +
592C LYS 4.5 0.9 - - - +
593C ARG* 1.3 72.6 - - - +
595C PRO* 1.3 81.7 + - + +
596C GLN* 3.3 4.5 + - + +
3004C GOL 5.1 14.5 + - - +
603D ASN* 3.0 17.7 - - - +
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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