Contacts of the helix formed by residues 414 - 424 (chain C) in PDB entry 2P5G
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 SER 414 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C LEU 3.5 2.2 + - - -
413C THR* 1.3 69.8 - - - +
415C LEU* 1.3 62.4 + - - +
416C TYR 3.5 2.0 - - - -
417C PRO* 3.1 16.9 - - - +
418C SER* 2.6 27.0 + - - -
479C PHE* 3.5 37.5 - - - -
482C ARG* 5.7 2.6 + - - -
563C ILE* 3.9 8.5 - - - +
564C ASN* 4.8 6.4 + - - -
115J A 5.1 1.8 - - - -
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Residues in contact with LEU 415 (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 LEU* 3.7 31.2 + - + -
413C THR 2.9 9.1 + - - -
414C SER* 1.3 73.0 - - - +
416C TYR* 1.3 78.6 + - + +
417C PRO* 4.1 0.2 - - - +
418C SER* 3.0 4.7 + - - -
419C ILE* 2.7 47.9 + - + +
590C GLY* 4.5 9.6 - - - +
622C THR* 3.5 27.1 - - - +
623C ASP* 3.8 23.6 - - + -
681C MSE 3.7 20.4 - - + -
115J A 4.1 11.9 + - - +
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Residues in contact with TYR 416 (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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393C GLY 4.4 0.2 - - - -
394C ALA* 3.7 27.0 + - - +
415C LEU* 1.3 99.4 - - + +
417C PRO* 1.3 77.1 - - + +
419C ILE* 3.1 11.5 + - + +
420C ILE* 3.0 28.9 + - - +
567C TYR* 3.5 58.6 - + + -
586C ILE* 3.8 20.1 - - + +
587C THR* 3.7 24.6 + - + +
590C GLY* 5.0 2.5 - - - -
622C THR* 5.4 1.3 - - - -
114J G 5.4 2.9 + - - -
115J A 3.6 31.8 + - - +
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Residues in contact with PRO 417 (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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414C SER* 3.1 19.5 - - - +
415C LEU 4.1 0.2 - - - +
416C TYR* 1.3 94.7 - - + +
418C SER* 1.3 60.2 + - - +
420C ILE* 3.3 13.0 + - + +
421C ARG* 3.1 29.1 + - - +
475C ILE* 4.0 17.5 - - + +
479C PHE* 4.3 4.0 - - + -
563C ILE* 3.5 45.1 - - + +
564C ASN* 5.2 4.0 - - - +
566C LEU* 5.3 2.2 - - + -
567C TYR* 5.6 3.4 - - + +
115J A 4.1 7.6 - - + +
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Residues in contact with SER 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C LEU* 6.5 0.7 - - - -
413C THR* 2.9 18.8 + - - -
414C SER* 2.6 31.6 + - - -
415C LEU* 3.2 7.4 - - - -
417C PRO* 1.3 72.1 - - - +
419C ILE* 1.3 52.1 + - - +
421C ARG* 3.3 15.1 + - - +
422C GLN* 2.8 38.2 + - - +
479C PHE* 4.9 4.9 - - - -
680C LEU* 3.5 26.3 + - - +
681C MSE 5.1 4.5 - - - -
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Residues in contact with ILE 419 (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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415C LEU* 2.7 41.4 + - + +
416C TYR* 3.5 16.2 - - + +
418C SER* 1.3 68.7 - - - +
420C ILE* 1.3 60.9 + - - +
422C GLN* 4.1 6.1 - - - -
423C VAL* 2.8 37.5 + - + +
425C ILE* 4.1 4.7 - - + -
586C ILE* 3.4 35.7 - - + +
589C PHE* 3.6 36.3 - - + -
590C GLY* 3.6 22.9 - - - +
681C MSE 4.4 2.9 - - - -
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Residues in contact with ILE 420 (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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416C TYR* 3.0 28.5 + - + +
417C PRO* 3.5 10.5 - - + +
418C SER 3.3 0.2 - - - -
419C ILE* 1.3 73.2 - - - +
421C ARG* 1.3 59.1 + - - +
424C ASN* 2.9 26.5 + - - -
425C ILE* 3.0 37.5 + - + +
471C VAL* 4.0 15.0 - - + -
472C PRO* 3.6 16.3 - - + +
475C ILE* 4.4 5.2 - - + -
566C LEU* 4.2 8.5 - - + -
567C TYR* 5.3 4.7 - - + -
570C LEU* 3.8 19.1 - - + -
586C ILE* 3.7 34.5 - - + -
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Residues in contact with ARG 421 (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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417C PRO 3.1 16.1 + - - +
418C SER* 3.7 12.1 + - - +
419C ILE 3.3 0.2 - - - -
420C ILE* 1.3 77.8 - - - +
422C GLN* 1.3 61.5 + - - +
424C ASN* 3.5 9.5 + - - +
472C PRO* 4.3 10.4 - - + +
475C ILE* 3.5 22.2 - - + -
476C THR* 3.0 48.4 + - - +
479C PHE* 4.7 31.7 - - - +
480C ASN* 5.5 1.6 + - - -
677C LYS* 4.7 7.3 - - - +
678C GLN* 4.8 9.7 + - - +
680C LEU* 3.3 51.3 - - + +
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Residues in contact with GLN 422 (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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418C SER 2.8 17.3 + - - +
419C ILE* 3.2 8.0 + - - +
421C ARG* 1.3 75.7 - - - +
423C VAL* 1.3 60.7 + - + +
424C ASN 3.1 0.4 + - - -
589C PHE* 3.4 15.6 - - - -
670C MSE 4.9 2.0 - - - +
671C CYS* 4.0 6.6 - - - +
676C ASN* 3.3 30.8 + - - +
677C LYS* 3.0 29.8 + - - +
678C GLN 2.8 22.0 + - - +
679C HIS* 3.2 11.5 + - - -
680C LEU* 2.8 39.5 + - + +
681C MSE 3.5 22.0 + - + +
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 2.8 24.7 + - + +
422C GLN* 1.3 72.0 - - - +
424C ASN* 1.3 70.3 + - - +
425C ILE* 3.5 22.4 - - + -
455C SER* 2.8 30.5 + - - +
456C CYS 3.7 16.6 - - - +
457C SER* 4.4 2.2 - - - -
463C TYR* 3.6 21.5 - - + +
589C PHE* 3.6 44.6 - - + -
676C ASN* 4.0 2.5 - - - +
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Residues in contact with ASN 424 (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 ILE 2.9 13.5 + - - -
421C ARG 3.5 3.4 + - - +
422C GLN 3.1 3.0 - - - -
423C VAL* 1.3 83.0 - - - +
425C ILE* 1.3 58.4 + - - +
429C THR* 2.8 35.5 + - - +
463C TYR* 3.5 5.8 - - - +
464C TYR 3.0 24.5 + - - +
467C ARG 3.4 16.5 + - - -
468C ASP* 4.0 2.4 - - - +
469C GLY 3.1 19.3 + - - +
472C PRO* 3.6 13.2 - - - +
677C LYS* 3.6 31.6 - - + +
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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