Contacts of the helix formed by residues 435 - 446 (chain C) in PDB entry 3ER8
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 TYR 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279C THR* 4.5 13.8 - - + +
320C HIS* 3.7 13.9 + + - -
425C LEU* 3.8 18.8 - - + +
428C GLN* 3.8 16.8 - - + -
429C MET* 3.9 38.4 - - + -
432C SER* 6.2 1.6 - - - -
433C GLY 3.1 23.9 + - - -
434C GLU* 1.3 76.6 + - - +
436C LYS* 1.3 121.1 + - + +
437C GLN 3.6 1.8 - - - -
438C CYS* 3.3 8.8 + - - +
439C LEU* 3.1 28.0 + - + +
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Residues in contact with LYS 436 (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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320C HIS* 3.1 46.3 + - + +
322C ILE* 4.9 10.7 - - + +
434C GLU* 5.8 2.7 - - - +
435C TYR* 1.3 125.1 + - + +
437C GLN* 1.3 64.5 + - - +
439C LEU* 3.1 20.1 + - + +
440C SER* 3.3 4.6 + - - -
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Residues in contact with GLN 437 (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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323C VAL* 5.8 1.2 - - - +
328C ARG* 4.6 10.5 - - - +
351C TYR* 5.0 6.1 - - + -
435C TYR 3.6 0.4 - - - -
436C LYS* 1.3 79.7 - - - +
438C CYS* 1.3 68.1 + - - +
440C SER* 2.8 34.2 + - - -
441C ASP* 2.6 42.4 + - - +
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Residues in contact with CYS 438 (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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331C MET* 3.1 22.4 - - + +
333C MET* 6.1 1.1 - - + -
351C TYR* 3.3 31.9 - - + -
352C PHE* 3.9 27.4 - - + -
421C CYS* 5.9 1.1 - - - -
425C LEU* 3.6 19.5 - - + -
434C GLU* 4.4 2.7 - - - -
435C TYR* 3.6 14.8 - - - +
437C GLN* 1.3 75.3 - - - +
439C LEU* 1.3 64.9 + - - +
441C ASP 3.1 0.7 + - - -
442C LEU* 2.7 21.3 + - - +
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Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C THR* 3.7 31.4 - - + +
282C LEU* 5.8 4.0 - - + -
283C LEU* 3.6 35.9 - - + +
286C ILE* 6.1 0.9 - - + -
316C VAL* 3.8 19.5 - - + -
320C HIS* 6.4 0.4 - - + -
322C ILE* 4.9 4.3 - - + -
425C LEU* 4.0 6.4 - - + +
429C MET* 5.7 1.3 - - + -
435C TYR* 3.1 19.5 + - + +
436C LYS* 3.1 13.0 - - + +
438C CYS* 1.3 77.7 - - - +
440C SER* 1.3 55.7 + - - +
442C LEU* 2.6 33.3 + - + +
443C LEU* 2.7 36.1 + - + +
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Residues in contact with SER 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ILE* 4.3 18.0 - - - +
323C VAL* 3.8 23.6 + - - +
328C ARG* 4.2 2.1 - - - +
436C LYS 3.3 3.6 + - - -
437C GLN* 2.8 34.3 + - - -
439C LEU* 1.3 76.7 - - - +
441C ASP* 1.3 65.3 + - - -
443C LEU* 2.9 21.6 + - - +
444C ASN* 3.0 22.5 + - - -
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Residues in contact with ASP 441 (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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328C ARG* 3.6 30.2 + - - +
329C ASN 3.0 18.2 - - - +
330C ASN* 4.6 2.4 - - - +
331C MET* 3.0 32.3 - - + +
351C TYR* 3.6 14.1 + - - -
437C GLN* 2.6 54.8 + - - +
438C CYS* 4.1 0.5 + - - -
440C SER* 1.3 71.4 + - - +
442C LEU* 1.3 52.9 + - - +
444C ASN* 3.7 0.7 + - - +
445C SER* 2.5 33.6 + - - -
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 4.6 2.2 - - + -
286C ILE* 3.7 31.2 - - + -
331C MET* 3.1 14.3 - - + +
418C ARG* 3.7 16.0 - - - +
421C CYS* 3.8 19.7 - - + -
422C ALA* 3.8 27.8 - - - +
425C LEU* 4.0 13.5 - - + -
438C CYS 2.7 12.0 + - - +
439C LEU* 2.6 29.6 + - + +
441C ASP* 1.3 70.1 - - - +
443C LEU* 1.3 64.6 + - + +
445C SER* 3.4 8.1 + - - -
446C MET* 3.0 29.9 - - + +
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Residues in contact with LEU 443 (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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141C MET* 2.6 28.1 - - + +
282C LEU* 4.5 13.9 - - + -
286C ILE* 5.8 1.1 - - + -
313C LEU* 3.5 27.6 - - + -
316C VAL* 4.1 8.3 - - + -
322C ILE* 3.4 32.5 - - + -
324C PHE* 3.7 15.9 - - + -
439C LEU* 2.7 43.5 + - + +
440C SER* 2.9 5.5 + - - +
442C LEU* 1.3 73.2 - - + +
444C ASN* 1.3 62.4 - - - +
446C MET* 2.9 29.7 + - + +
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Residues in contact with ASN 444 (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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322C ILE* 5.3 0.2 - - - +
323C VAL* 3.2 27.0 + - - +
324C PHE* 3.7 3.4 - - - +
325C ASP* 3.5 20.8 - - - +
326C GLY 4.3 8.6 - - - +
328C ARG* 3.0 46.9 - - + +
440C SER* 3.0 13.3 + - - +
441C ASP 4.0 0.7 - - - +
443C LEU* 1.3 80.7 - - - +
445C SER* 1.3 61.4 + - - +
446C MET 2.9 1.6 + - - -
447C MET* 3.0 44.4 + - - +
449C ARG* 5.0 0.3 - - - -
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Residues in contact with SER 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C GLY 5.9 0.2 - - - -
328C ARG 4.0 7.5 + - - -
331C MET* 2.9 21.7 - - - +
332C PRO* 3.4 19.9 - - - +
418C ARG* 3.1 19.2 + - - -
441C ASP 2.5 23.7 + - - -
442C LEU 3.5 8.5 - - - -
443C LEU 3.2 0.4 + - - -
444C ASN* 1.3 76.0 - - - +
446C MET* 1.3 56.0 + - - +
447C MET 3.4 0.2 - - - -
449C ARG* 2.8 32.9 + - - +
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Residues in contact with MET 446 (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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141C MET* 3.3 43.2 - - + +
144C SER* 3.2 20.8 + - - -
145C MET* 6.0 9.4 - - + +
282C LEU* 6.1 1.3 - - + -
286C ILE* 4.1 17.7 - - + -
313C LEU* 4.8 1.1 - - + -
418C ARG* 2.8 42.4 - - - +
442C LEU* 3.0 23.1 - - + +
443C LEU* 2.9 48.8 + - + +
445C SER* 1.3 75.8 - - - +
447C MET* 1.3 57.0 + - - +
449C ARG* 3.9 3.4 - - - -
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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