Contacts of the helix formed by residues 471 - 479 (chain I) in PDB entry 6PSS
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 VAL 471 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I PHE* 5.9 4.9 - - + -
124I MET* 5.9 1.3 - - + -
467I GLY 3.3 10.9 + - - +
468I LEU* 4.3 17.3 - - + +
470I ARG* 1.3 77.5 - - - +
472I GLU* 1.3 65.8 + - - +
473I ARG 3.3 0.9 - - - -
474I ALA* 3.5 8.2 + - + +
475I VAL* 3.5 20.7 - - + +
492I MET 4.8 2.2 - - - +
493I ILE* 4.1 22.0 - - + -
494I ASN* 3.5 40.8 - - - +
497I PRO* 4.2 6.7 - - + +
498I ILE* 3.8 20.9 - - + -
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Residues in contact with GLU 472 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I VAL* 3.4 30.6 - - + +
58I PRO 5.3 0.5 - - - +
59I ILE* 3.7 28.8 - - + +
468I LEU 3.3 19.3 - - - +
469I VAL* 3.3 23.8 + - - +
471I VAL* 1.3 81.3 - - - +
473I ARG* 1.3 59.5 + - + +
476I LYS* 3.1 50.6 + - + +
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Residues in contact with ARG 473 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469I VAL* 3.4 39.7 + - + +
470I ARG* 3.7 40.5 + - - +
471I VAL 3.3 0.6 - - - -
472I GLU* 1.3 76.7 - - + +
474I ALA* 1.3 62.7 + - - +
476I LYS* 4.3 3.4 - - - -
477I GLU* 3.7 22.7 + - - +
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Residues in contact with ALA 474 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470I ARG 4.5 3.2 + - - +
471I VAL* 3.5 13.0 + - - +
472I GLU 3.2 0.6 - - - -
473I ARG* 1.3 80.4 - - - +
475I VAL* 1.3 58.5 + - + +
477I GLU* 3.1 4.1 + - - +
478I ARG* 2.6 37.5 + - + +
492I MET 4.3 9.0 - - - +
494I ASN* 4.9 13.5 - - - +
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Residues in contact with VAL 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ILE* 4.5 12.2 - - + +
68I LEU* 3.7 28.9 - - + -
471I VAL* 3.5 20.6 + - + +
472I GLU 4.7 0.2 - - - +
474I ALA* 1.3 75.4 - - + +
476I LYS* 1.3 64.9 + - - +
477I GLU 3.2 0.7 - - - -
478I ARG* 3.9 5.6 - - - +
479I LEU* 3.2 29.2 + - + +
492I MET* 3.4 56.3 - - + +
493I ILE* 4.4 9.2 - - + -
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Residues in contact with LYS 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ILE* 3.9 11.0 - - + +
60I GLN* 3.3 39.0 + - - +
61I SER* 4.1 11.4 + - - +
62I TYR 4.4 0.7 + - - -
472I GLU* 3.1 37.6 + - + +
473I ARG* 4.6 4.9 - - - +
475I VAL* 1.3 80.4 - - - +
477I GLU* 1.3 74.7 + - + +
479I LEU 4.3 0.2 - - - -
480I SER* 3.8 17.2 + - - -
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Residues in contact with GLU 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I TYR* 5.4 5.5 + - - +
473I ARG 3.7 17.3 - - - +
474I ALA* 3.1 4.4 + - - +
476I LYS* 1.3 103.5 - - + +
478I ARG* 1.3 61.9 + - - +
480I SER* 4.1 14.1 + - - +
481I LEU* 3.7 21.5 + - - +
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Residues in contact with ARG 478 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474I ALA 2.6 21.6 + - - +
475I VAL* 4.2 7.2 - - - -
477I GLU* 1.3 74.8 - - - +
479I LEU* 1.3 61.0 + - - +
480I SER 3.2 0.4 - - - -
481I LEU* 2.6 32.7 + - - +
483I ASP 4.4 2.0 - - - +
484I LEU* 4.0 19.2 - - - +
487I LEU* 3.4 44.5 - - - +
491I ASP 5.9 1.1 - - - -
492I MET* 3.7 31.6 - - + +
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Residues in contact with LEU 479 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ILE* 4.9 5.4 - - + +
61I SER* 3.8 11.5 - - - -
66I SER* 2.8 45.3 + - - +
67I GLU 4.3 0.9 - - - +
68I LEU* 4.1 24.9 - - + +
102I LEU* 3.7 35.0 - - + -
104I ILE* 5.4 1.6 - - + -
475I VAL* 3.2 24.4 + - + +
478I ARG* 1.3 79.9 - - - +
480I SER* 1.3 56.7 + - - +
481I LEU 3.4 0.4 - - - -
483I ASP* 2.9 15.0 - - - +
487I LEU* 3.8 11.7 - - + -
492I MET* 3.7 24.5 - - + -
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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