Contacts of the helix formed by residues 444 - 459 (chain C) in PDB entry 3U1K
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 444 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429C PHE* 5.6 1.6 + - - +
439C LYS 5.8 2.0 + - - -
441C THR 6.0 0.4 - - - +
442C GLY* 4.0 5.1 - - - -
443C LEU* 1.3 76.3 - - - +
445C ARG* 1.3 62.0 + - - +
446C ARG* 3.1 12.7 + - - +
447C GLU* 2.8 55.0 + - - +
448C LEU* 3.1 21.1 + - - +
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Residues in contact with ARG 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B THR* 5.3 11.5 + - - +
100C VAL 5.9 0.6 + - - -
101C ASP* 4.8 13.6 + - - -
123C THR* 4.3 14.3 + - - -
128C ILE* 3.9 36.0 - - + +
131C SER* 6.0 4.9 - - - -
132C ARG* 3.7 24.1 - - - +
443C LEU* 3.6 30.3 + - + +
444C ASN* 1.3 73.8 + - - +
446C ARG* 1.3 58.1 + - - +
448C LEU* 3.3 4.9 + - - +
449C GLY 2.9 23.0 + - - -
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Residues in contact with ARG 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C CIT 2.6 55.7 + - - +
132C ARG* 3.5 12.7 - - - +
427C TYR* 5.8 0.4 - - + -
429C PHE* 5.3 7.2 - - + -
444C ASN* 3.1 8.2 + - - +
445C ARG* 1.3 78.2 - - - +
447C GLU* 1.3 60.1 + - + +
449C GLY* 3.2 0.7 + - - -
450C HIS* 2.9 57.6 + - + +
670C CIT 2.7 42.3 + - - +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C HIS* 5.9 1.0 - - - -
427C TYR* 3.5 34.7 + - + +
428C GLU* 3.5 13.8 - - - +
429C PHE* 2.6 48.2 + - + +
430C PRO* 5.1 0.3 - - - +
444C ASN* 2.8 43.5 + - - +
446C ARG* 1.3 78.8 - - + +
448C LEU* 1.3 58.6 + - - +
451C GLY* 3.0 24.6 + - - -
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Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C THR 5.7 0.2 - - - +
124C SER 5.4 0.2 - - - -
125C ASP* 3.1 46.7 - - + +
128C ILE* 4.0 19.1 - - + -
129C LEU* 3.8 22.9 - - + -
443C LEU* 4.5 19.3 - - + -
444C ASN 3.1 12.8 + - - +
445C ARG* 3.5 8.5 - - - +
446C ARG 3.2 0.2 - - - -
447C GLU* 1.3 75.6 - - - +
449C GLY* 1.3 59.2 + - - +
451C GLY* 3.4 1.3 + - - -
452C ALA* 2.9 27.8 + - + +
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Residues in contact with GLY 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 3.9 18.1 - - - +
132C ARG* 4.0 14.8 - - - +
445C ARG 2.9 14.6 + - - -
446C ARG 3.2 3.1 + - - -
448C LEU* 1.3 76.6 - - - +
450C HIS* 1.3 65.5 + - - +
452C ALA* 3.4 3.6 + - - +
453C LEU* 3.1 22.9 + - - +
558C GLN* 4.7 7.6 + - - -
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Residues in contact with HIS 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C CIT 2.5 38.6 + - - -
132C ARG* 4.2 3.4 - - - -
427C TYR* 3.1 44.9 + - + -
429C PHE* 5.4 0.4 - + - -
446C ARG* 2.9 35.7 + - + +
449C GLY* 1.3 75.7 - - - +
451C GLY* 1.3 65.6 + - - +
453C LEU* 3.3 7.0 + - + +
454C ALA* 3.1 24.1 + - - +
483C SER* 3.8 0.6 + - - -
484C SER* 4.0 8.0 - - - -
546C LYS* 4.3 3.6 - - - -
558C GLN* 4.8 2.9 - - - -
670C CIT 2.9 44.2 + - - -
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Residues in contact with GLY 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 3.7 20.0 - - - +
426C HIS* 5.2 0.2 - - - -
427C TYR* 3.5 25.0 - - - +
447C GLU 3.0 14.3 + - - -
448C LEU* 3.8 1.6 - - - -
450C HIS* 1.3 74.3 - - - +
452C ALA* 1.3 58.2 - - - +
454C ALA 3.4 1.0 + - - -
455C GLU* 2.9 32.1 + - - +
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Residues in contact with ALA 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 3.8 32.3 - - + -
448C LEU* 2.9 19.6 + - + +
449C GLY 3.6 5.2 - - - +
450C HIS 3.3 0.2 - - - -
451C GLY* 1.3 74.8 - - - +
453C LEU* 1.3 57.7 + - - +
455C GLU* 3.4 10.1 + - - +
456C LYS* 3.0 36.7 + - + +
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Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C GLY 3.1 12.8 + - - +
450C HIS* 3.6 9.0 - - - +
451C GLY 3.2 0.6 - - - -
452C ALA* 1.3 75.1 - - - +
454C ALA* 1.3 65.9 + - - +
456C LYS* 3.3 20.5 - - + +
457C ALA* 3.1 19.8 + - - +
484C SER* 3.5 25.1 - - - +
485C MET* 3.6 19.1 - - + -
546C LYS* 4.2 11.4 - - + +
556C ALA* 3.9 21.5 - - + -
557C LEU 4.6 0.7 - - - +
558C GLN* 3.9 49.6 - - + +
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Residues in contact with ALA 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 4.0 17.9 - - + -
427C TYR* 5.7 0.4 - - + -
450C HIS 3.1 15.1 + - - +
451C GLY 4.0 2.0 - - - +
453C LEU* 1.3 77.6 - - - +
455C GLU* 1.3 62.9 + - - +
457C ALA* 3.1 16.7 + - - +
458C LEU* 3.2 19.4 + - - +
484C SER 3.7 22.0 + - - +
485C MET* 5.5 0.7 - - - -
487C SER* 3.9 16.4 - - - -
488C ALA* 4.0 6.7 - - - +
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Residues in contact with GLU 455 (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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419C LYS* 2.7 38.3 + - - +
423C PHE* 3.5 24.7 - - + +
424C MET* 3.4 9.2 - - - +
425C LEU* 2.9 43.0 + - + +
451C GLY 2.9 18.6 + - - +
452C ALA* 3.5 9.4 - - - +
454C ALA* 1.3 76.7 - - - +
456C LYS* 1.3 58.5 + - + +
458C LEU 3.2 1.2 + - - -
459C TYR* 2.8 29.8 + - + +
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Residues in contact with LYS 456 (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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230C GLU* 2.7 39.2 + - - +
231C ALA 3.2 30.8 + - - -
232C SER* 3.6 21.9 + - - +
452C ALA* 3.0 23.6 + - + +
453C LEU* 3.3 22.6 - - - +
455C GLU* 1.3 75.6 - - + +
457C ALA* 1.3 64.3 + - - +
459C TYR* 4.0 9.7 - - + +
460C PRO* 3.4 15.6 - - - +
555C THR 3.5 11.6 - - - +
556C ALA* 3.9 9.0 - - + -
557C LEU 4.4 1.0 + - - -
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Residues in contact with ALA 457 (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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453C LEU 3.1 14.3 + - - +
454C ALA* 3.3 11.0 - - - +
455C GLU 3.1 0.4 - - - -
456C LYS* 1.3 80.4 - - - +
458C LEU* 1.3 59.0 + - - +
460C PRO* 3.7 1.7 - - - +
485C MET* 5.6 1.8 - - + -
488C ALA* 4.0 15.5 - - + -
506C VAL* 3.8 11.5 - - + +
548C ALA* 3.8 26.9 - - + -
555C THR* 2.9 29.5 + - - +
556C ALA* 3.8 7.4 - - + -
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Residues in contact with LEU 458 (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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423C PHE* 3.8 20.4 - - + -
425C LEU* 3.7 30.3 - - + -
454C ALA 3.2 10.6 + - - +
455C GLU 3.9 0.2 - - - +
457C ALA* 1.3 76.7 - - - +
459C TYR* 1.3 65.2 + - - +
460C PRO* 2.9 6.6 - - - -
461C VAL* 3.0 25.7 + - + +
462C ILE* 3.4 6.1 - - + +
472C VAL* 5.0 1.1 - - + -
488C ALA* 3.3 31.2 - - - +
491C GLY* 4.0 14.8 - - - -
492C SER* 3.8 11.9 - - - +
495C LEU* 4.5 11.7 - - + -
506C VAL* 3.6 26.5 - - + -
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Residues in contact with TYR 459 (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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232C SER* 5.6 4.7 - - - -
234C GLU* 3.4 23.8 - - - -
420C ASP* 2.5 46.3 + - + +
421C LYS* 2.8 50.7 + - + -
423C PHE* 3.9 13.2 - + + -
455C GLU* 2.8 20.4 + - + +
456C LYS* 4.0 9.2 - - - -
458C LEU* 1.3 75.8 - - - +
460C PRO* 1.3 67.6 - - + +
462C ILE* 3.3 17.3 + - - +
464C ARG* 3.9 4.0 + - - -
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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
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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