Contacts of the helix formed by residues 512 - 526 (chain C) in PDB entry 2A2N
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 CYS 512 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508C PHE 2.9 13.8 + - - +
509C PRO 3.7 2.2 - - - -
511C GLU* 1.3 81.1 - - - +
513C PRO* 1.3 65.1 - - - +
515C THR* 4.0 11.4 - - - -
516C VAL* 2.9 22.9 + - + +
565C GLU* 2.9 43.1 - - - +
567C HIS* 5.4 0.4 - - - -
570C LEU* 3.7 15.7 - - - -
607C THR* 4.1 2.7 - - - -
608C VAL 3.3 25.4 - - - -
609C PHE* 4.2 7.2 - - + -
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Residues in contact with PRO 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C VAL* 3.6 10.0 - - + +
509C PRO* 3.1 20.9 - - + +
510C VAL 3.8 6.5 - - - +
511C GLU 3.3 9.6 - - - +
512C CYS* 1.3 87.6 - - - +
514C LYS* 1.3 63.3 + - + +
517C GLU* 2.9 31.6 + - - +
565C GLU* 3.3 10.8 - - - +
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Residues in contact with LYS 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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513C PRO* 1.3 82.6 - - + +
515C THR* 1.3 58.0 + - - +
517C GLU* 4.3 9.1 + - - +
518C ASN* 2.9 31.0 + - - +
558C TRP* 3.5 33.8 - - + +
562C PHE* 4.2 13.2 - - + -
563C GLU* 4.2 22.2 - - - +
565C GLU* 2.9 20.3 + - + +
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Residues in contact with THR 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C CYS* 3.8 9.0 - - - -
514C LYS* 1.3 75.5 - - - +
516C VAL* 1.3 62.6 + - - +
518C ASN* 3.4 2.9 + - - +
519C PHE* 3.0 22.9 + - - +
562C PHE* 3.6 18.8 - - + -
563C GLU 4.6 0.7 + - - -
565C GLU* 2.6 31.8 + - - +
580C MET* 3.6 24.1 - - + +
588C ASN* 5.7 0.2 - - - -
607C THR* 3.5 14.8 + - + +
609C PHE* 3.4 37.9 - - + -
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Residues in contact with VAL 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C VAL* 4.0 5.2 - - + -
491C SER 3.5 24.5 - - - +
507C LEU* 3.9 11.0 - - + -
508C PHE 3.6 15.0 - - - +
509C PRO* 3.6 33.0 - - + -
512C CYS 2.9 19.8 + - - +
515C THR* 1.3 74.3 - - - +
517C GLU* 1.3 59.4 + - - +
519C PHE* 3.2 5.4 + - - +
520C CYS* 2.8 41.8 + - - -
609C PHE* 4.0 18.4 - - + +
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Residues in contact with GLU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ARG* 2.8 47.7 + - + +
490C VAL* 3.5 14.9 - - + +
513C PRO 2.9 19.5 + - - +
514C LYS* 3.6 15.4 + - - +
516C VAL* 1.3 73.9 - - - +
518C ASN* 1.3 63.4 + - - +
520C CYS* 4.1 2.4 - - - +
521C VAL* 2.9 32.6 + - + +
557C ILE* 4.1 7.2 - - + -
558C TRP* 3.8 19.1 + - + -
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Residues in contact with ASN 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C LYS 2.9 17.2 + - - +
515C THR 3.6 5.1 + - - +
517C GLU* 1.3 75.1 - - - +
519C PHE* 1.3 64.6 + - - +
522C HIS* 3.0 36.4 + - - +
528C TYR* 4.4 2.8 + - - -
556C SER* 3.2 6.3 - - - -
557C ILE* 2.9 45.9 + - - +
558C TRP* 4.0 5.3 - - + -
562C PHE* 3.6 23.1 - - + -
580C MET* 4.4 6.7 - - - +
589C GLY 2.9 23.0 + - - -
590C SER* 4.4 3.4 - - - +
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Residues in contact with PHE 519 (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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494C ALA* 4.0 23.6 - - + -
496C ILE* 4.3 13.2 - - + -
505C THR* 4.8 0.7 - - - -
507C LEU* 4.0 24.2 - - + -
515C THR 3.0 17.9 + - - +
516C VAL* 3.7 3.1 - - - +
518C ASN* 1.3 82.1 - - - +
520C CYS* 1.3 61.5 + - - +
522C HIS* 3.8 1.7 - - - +
523C SER* 2.9 40.9 + - - -
528C TYR* 4.0 17.9 - + - +
578C LEU* 4.7 6.5 - - + -
580C MET* 6.1 1.6 - - - -
592C PHE* 3.9 29.2 - + - -
609C PHE* 3.7 30.5 - + + -
643C ILE* 4.0 25.1 - - + -
645C VAL* 5.6 0.2 - - + -
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Residues in contact with CYS 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ARG 3.4 19.7 - - - +
490C VAL 4.3 0.2 - - - -
491C SER 3.7 24.7 - - - -
507C LEU* 3.7 17.3 - - - -
516C VAL* 2.8 33.7 + - - +
517C GLU 4.1 0.7 - - - +
519C PHE* 1.3 72.2 - - - +
521C VAL* 1.3 60.9 + - - +
523C SER* 3.2 2.1 + - - -
524C ARG* 2.9 39.9 + - - +
645C VAL* 3.8 23.5 - - + +
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Residues in contact with VAL 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ARG* 3.5 57.0 - - + +
517C GLU* 2.9 20.1 + - + +
520C CYS* 1.3 74.5 - - - +
522C HIS* 1.3 66.2 + - - +
523C SER 3.3 0.2 + - - -
524C ARG* 3.3 9.2 + - - +
525C ASN* 2.8 48.9 + - - +
557C ILE* 3.8 24.7 - - + -
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C ASN* 3.0 32.3 + - - +
519C PHE 3.8 0.2 - - - +
521C VAL* 1.3 75.7 - - - +
523C SER* 1.3 64.5 + - - +
525C ASN* 3.3 6.0 + - - +
526C GLY 3.1 3.5 + - - -
527C TYR* 2.9 63.4 + + + +
528C TYR* 3.5 34.1 - - + -
555C GLU* 2.8 29.2 + - + -
556C SER* 3.7 8.4 - - - -
557C ILE* 3.5 21.0 - - + +
590C SER* 3.9 6.7 - - - -
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Residues in contact with SER 523 (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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519C PHE* 2.9 28.5 + - - -
520C CYS* 3.5 4.5 - - - -
521C VAL 3.2 0.4 - - - -
522C HIS* 1.3 76.8 - - - +
524C ARG* 1.3 56.6 + - - +
526C GLY* 3.0 19.2 + - - -
527C TYR 5.1 0.4 - - - +
528C TYR* 3.8 8.9 - - - +
529C ASN* 4.7 3.1 - - - +
642C ASN* 6.0 0.2 - - - +
643C ILE* 3.3 51.2 + - - +
645C VAL* 3.5 19.3 - - - -
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Residues in contact with ARG 524 (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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488C LYS 5.4 0.8 + - - -
489C ARG* 2.8 44.3 + - - +
490C VAL 4.1 7.3 + - - -
491C SER* 4.3 1.8 - - - -
520C CYS* 2.9 28.9 + - - +
521C VAL* 3.8 8.6 - - - +
523C SER* 1.3 74.2 - - - +
525C ASN* 1.3 64.4 + - - +
526C GLY 3.1 1.1 + - - -
643C ILE 5.2 1.1 - - - -
645C VAL* 3.5 39.0 + - + +
646C LYS 4.7 3.4 + - - -
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Residues in contact with ASN 525 (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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521C VAL* 2.8 41.0 + - - +
522C HIS* 3.7 9.5 + - - +
523C SER 3.2 0.2 - - - -
524C ARG* 1.3 78.9 - - - +
526C GLY* 1.3 60.6 + - - +
527C TYR* 3.4 5.5 + - + +
557C ILE* 5.3 2.6 - - - +
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Residues in contact with GLY 526 (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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522C HIS 3.1 0.2 + - - -
523C SER 3.0 14.4 + - - -
524C ARG 3.1 2.5 + - - -
525C ASN* 1.3 79.5 - - - +
527C TYR* 1.3 63.9 + - - +
528C TYR 3.2 3.4 - - - -
529C ASN* 3.1 44.0 + - - +
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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
------------------------------------------------------------
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