Contacts of the strand formed by residues 469 - 472 (chain H) in PDB entry 4E2I
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 469 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408H PHE* 3.7 30.3 - - + -
412H MET* 4.0 9.0 - - - -
439H LEU 4.7 1.6 - - - +
440H LEU* 3.5 30.5 - - + -
443H CYS* 3.5 26.5 - - + -
444H GLY 3.4 17.4 + - - +
445H GLY* 3.8 1.4 - - - -
446H LYS 3.4 18.0 + - - +
467H GLN* 3.9 2.9 - - - +
468H PHE* 1.3 86.0 + - + +
470H VAL* 1.3 66.0 + - - +
471H VAL* 4.3 7.0 - - + -
522H PRO* 4.1 1.5 - - - +
523H PRO 3.0 11.7 - - - +
524H GLY* 3.9 8.7 - - - -
525H ILE* 6.1 1.3 - - + +
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Residues in contact with VAL 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H TYR* 4.6 6.0 - - + +
446H LYS 3.4 4.7 - - - +
448H LEU* 3.5 39.0 - - + +
464H ALA* 3.7 28.5 - - + -
467H GLN* 5.7 0.2 - - + -
469H LEU* 1.3 78.0 - - - +
471H VAL* 1.3 65.6 + - - +
472H PHE* 4.1 19.5 - - + -
521H PHE* 4.1 7.9 - - + -
522H PRO* 3.9 12.3 - - + +
523H PRO 2.8 15.7 + - - +
524H GLY* 3.1 1.9 - - - -
525H ILE 2.8 31.1 + - - -
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Residues in contact with VAL 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505G VAL* 5.0 1.8 - - + -
436H ALA* 3.7 30.7 - - + +
440H LEU* 3.5 32.1 - - + -
446H LYS 3.3 4.2 + - - -
447H ALA* 3.4 17.3 - - + +
448H LEU 2.9 26.4 + - - +
469H LEU* 4.3 4.9 - - + -
470H VAL* 1.3 83.7 - - - +
472H PHE* 1.3 62.1 + - - +
473H GLU* 3.4 25.8 + - - +
525H ILE* 3.4 14.8 - - + +
527H THR* 5.1 0.9 - - + -
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Residues in contact with PHE 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H TYR* 3.7 25.1 - + - -
448H LEU* 3.6 28.3 - - + -
449H ASN* 4.8 0.9 - - - +
450H VAL* 3.6 33.7 - - + -
461H LEU* 4.4 12.1 - - + -
470H VAL* 4.1 13.5 - - + -
471H VAL* 1.3 69.9 - - - +
473H GLU* 1.3 62.1 + - - +
475H VAL* 4.3 9.4 - - + -
494H LEU* 4.2 13.9 - - + -
497H LEU* 5.3 5.6 - - + -
501H LEU* 4.9 4.9 - - + -
521H PHE* 4.4 14.4 - + - -
525H ILE 2.9 11.2 + - - +
526H VAL* 3.5 37.2 - - + -
527H THR* 2.8 34.3 + - - +
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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