Contacts of the strand formed by residues 510 - 516 (chain C) in PDB entry 5I4A
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 ASN 510 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439C LYS* 3.5 10.1 + - - +
440C ASN* 2.9 26.6 + - - +
441C LEU 2.9 25.1 + - - -
508C PRO* 3.9 2.5 - - - +
509C GLU* 1.3 98.7 - - - +
511C VAL* 1.3 67.5 + - - +
512C PHE* 4.1 14.1 - - + -
536C LYS* 4.2 13.8 - - - -
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Residues in contact with VAL 511 (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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441C LEU* 3.5 7.4 - - + +
443C ILE* 4.0 10.3 - - + -
493C TYR* 3.5 32.5 - - + +
497C PHE* 4.0 9.4 - - + -
508C PRO* 4.5 7.0 - - + -
510C ASN* 1.3 78.0 - - - +
512C PHE* 1.3 65.8 + - - +
513C ILE* 3.6 30.7 + - + +
530C ILE* 4.8 6.8 - - + +
535C THR* 3.7 23.8 - - + -
536C LYS 4.0 13.8 - - - -
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Residues in contact with PHE 512 (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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440C ASN* 4.0 22.9 - - + -
441C LEU 2.8 11.0 + - - +
442C TYR* 3.5 46.2 - + + -
443C ILE* 2.9 33.8 + - - +
510C ASN* 4.3 11.0 - - + -
511C VAL* 1.3 75.1 - - - +
513C ILE* 1.3 61.2 + - - +
514C LEU* 3.8 19.1 - - + -
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Residues in contact with ILE 513 (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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443C ILE* 3.8 24.9 - - + -
445C ILE* 4.1 18.4 - - + -
493C TYR* 4.0 9.6 - - + -
511C VAL* 3.6 30.7 + - + +
512C PHE* 1.3 74.8 - - - +
514C LEU* 1.3 65.3 + - - +
515C ARG 3.9 1.7 + - - -
519C PHE* 4.0 31.1 - - + -
526C ILE* 5.7 2.7 - - + -
530C ILE* 4.1 28.9 - - + -
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Residues in contact with LEU 514 (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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442C TYR* 5.3 9.0 - - + -
443C ILE 2.8 24.2 + - - +
444C GLY* 3.3 5.8 - - - -
445C ILE* 2.8 34.6 + - - +
512C PHE* 4.1 27.1 - - + +
513C ILE* 1.3 78.8 - - - +
515C ARG* 1.3 56.1 + - - +
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Residues in contact with ARG 515 (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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445C ILE* 3.7 23.4 - - + +
447C LEU* 3.3 39.1 + - - +
449C HIS* 4.6 2.0 + - - -
489C LEU* 5.5 1.8 - - - +
513C ILE 3.9 1.6 + - - -
514C LEU* 1.3 73.0 - - - +
516C ASP* 1.3 73.3 + - - +
517C GLY 3.0 30.7 + - - +
518C ARG 3.8 16.6 + - - +
519C PHE* 3.5 48.9 - - + +
520C ILE* 4.6 2.4 - - - +
521C GLU* 2.6 46.4 + - - -
526C ILE* 5.2 0.8 - - - +
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Residues in contact with ASP 516 (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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445C ILE 2.9 19.9 + - - +
446C ASP* 3.9 28.7 - - + +
447C LEU 5.2 3.0 + - - +
514C LEU 4.2 0.2 + - - -
515C ARG* 1.3 79.1 + - - +
517C GLY* 1.3 63.1 + - - +
518C ARG 4.1 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