Contacts of the helix formed by residues 425 - 434 (chain C) in PDB entry 4X4R
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 VAL 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321C LYS* 4.5 6.5 - - + -
328C TYR* 3.5 44.0 - - + -
330C LEU* 4.0 18.4 - - + -
420C LEU* 3.8 35.2 - - + +
421C PHE* 5.6 0.4 - - - -
423C GLU* 2.7 11.8 + - + +
424C PRO* 1.3 78.0 - - + +
426C THR* 1.3 65.8 + - - +
427C ALA 3.4 1.8 - - - -
428C GLU* 3.3 10.4 + - - +
429C LEU* 3.0 38.8 + - + +
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Residues in contact with THR 426 (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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260C LEU 4.7 2.9 - - - +
262C ILE* 3.4 44.3 + - + +
263C GLU 5.5 0.4 - - - +
264C PRO* 5.9 2.4 - - + +
267C LEU* 4.2 21.4 - - + +
321C LYS* 5.5 0.2 - - - +
421C PHE* 4.0 16.3 + - - -
423C GLU 4.1 4.7 + - - -
424C PRO* 3.7 2.0 - - - +
425C VAL* 1.3 78.1 - - - +
427C ALA* 1.3 65.2 + - - +
429C LEU* 3.3 3.6 + - - +
430C CYS* 3.2 23.9 + - - -
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Residues in contact with ALA 427 (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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259C PRO 4.1 17.7 - - - +
260C LEU* 4.0 16.2 - - + +
321C LYS* 4.9 6.7 - - - +
425C VAL 3.4 0.4 - - - -
426C THR* 1.3 80.4 - - - +
428C GLU* 1.3 74.1 + - - +
430C CYS* 3.5 4.5 + - - +
431C GLU* 3.1 22.2 + - - +
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Residues in contact with GLU 428 (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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319C ALA* 4.7 5.7 - - + +
320C PHE 4.0 20.3 - - - +
321C LYS* 3.3 49.1 + - + +
330C LEU* 3.7 21.5 - - + -
425C VAL* 3.3 6.6 + - - +
426C THR 3.2 0.4 - - - -
427C ALA* 1.3 83.3 + - - +
429C LEU* 1.3 61.4 + - - +
431C GLU* 3.4 7.4 + - - +
432C MET* 2.8 30.2 + - - +
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Residues in contact with LEU 429 (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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267C LEU* 3.8 27.4 - - + -
278C VAL* 3.7 20.2 - - + -
330C LEU* 4.1 19.5 - - + -
420C LEU* 4.4 11.0 - - + +
421C PHE* 4.3 15.3 - - + -
425C VAL* 3.0 35.0 + - + +
426C THR* 3.3 4.0 + - - +
428C GLU* 1.3 73.2 - - - +
430C CYS* 1.3 61.8 + - - +
432C MET* 3.1 28.0 + - + +
433C MET* 2.8 45.3 + - + +
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Residues in contact with CYS 430 (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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260C LEU* 3.4 26.0 - - + -
262C ILE* 3.6 33.2 - - + -
267C LEU* 3.6 24.9 - - - -
426C THR* 3.2 19.3 + - - +
427C ALA 3.9 0.2 - - - +
429C LEU* 1.3 77.9 - - - +
431C GLU* 1.3 57.3 + - - +
433C MET* 5.0 0.4 - - - -
434C GLY* 2.9 7.8 + - - -
435C VAL* 2.9 47.4 + - + +
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Residues in contact with GLU 431 (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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366A ARG* 4.1 20.8 + - - -
368A PHE* 6.1 0.3 - - - +
237C ARG* 5.5 5.0 + - - -
260C LEU* 4.2 8.5 - - + +
317C ARG* 3.4 20.1 + - - +
427C ALA 3.1 14.4 + - - +
428C GLU* 3.5 11.2 - - - +
429C LEU 3.2 0.2 - - - -
430C CYS* 1.3 77.4 - - - +
432C MET* 1.3 62.7 + - - +
434C GLY* 3.3 11.0 + - - -
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Residues in contact with MET 432 (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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377A PHE* 3.9 3.8 - - - -
278C VAL* 4.6 2.5 - - + -
317C ARG* 3.2 68.6 + - + +
318C SER* 3.9 5.8 - - - +
319C ALA* 3.6 29.8 - - + -
330C LEU* 4.0 11.7 - - + +
331C PHE 4.5 5.4 - - - -
332C GLU* 4.3 20.9 - - + +
428C GLU 2.8 17.8 + - - +
429C LEU* 3.5 34.1 - - + +
431C GLU* 1.3 78.1 - - - +
433C MET* 1.3 67.1 + - + +
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Residues in contact with MET 433 (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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365A PHE* 3.8 3.5 - - - -
377A PHE* 3.6 7.3 - - - -
267C LEU* 3.7 30.5 - - + -
270C ILE* 4.1 13.5 - - + -
271C VAL* 4.2 22.9 - - + -
274C ARG* 2.5 50.9 + - - +
278C VAL* 4.4 8.5 - - + -
332C GLU* 3.8 31.4 - - - +
429C LEU* 2.8 30.3 + - + +
432C MET* 1.3 81.8 - - + +
434C GLY* 1.3 62.6 + - - +
435C VAL* 3.6 10.2 + - + -
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Residues in contact with GLY 434 (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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365A PHE* 3.8 3.0 - - - -
366A ARG* 2.8 54.0 + - - +
377A PHE* 4.9 1.3 - - - -
317C ARG* 5.5 1.1 - - - -
430C CYS 2.9 6.5 + - - -
431C GLU* 3.3 8.0 + - - -
432C MET 3.3 4.4 + - - -
433C MET* 1.3 79.6 - - - +
435C VAL* 1.3 67.2 + - - +
436C LYS 3.2 1.2 + - - -
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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