Contacts of the helix formed by residues 397 - 409 (chain C) in PDB entry 1EAK
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 LEU 397 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C THR* 4.9 0.4 - - + -
135C LEU* 4.2 19.7 - - + -
140C VAL* 3.8 22.0 - - + -
143C ALA* 4.2 11.2 - - + -
144C PHE* 3.4 32.8 - - + -
173C PHE* 3.6 15.9 - - + -
207C PHE* 3.4 35.9 - - + -
213C TRP* 3.7 22.4 - - + -
214C THR 3.0 9.7 + - - +
215C LEU* 4.8 1.9 - - + +
395C TYR 3.2 1.2 + - - -
396C SER* 1.3 72.3 + - - +
398C PHE* 1.3 55.1 + - - +
401C ALA* 2.7 38.6 + - - +
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Residues in contact with PHE 398 (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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143C ALA* 3.8 17.1 - - + +
146C ARG* 3.4 44.6 - - + +
147C ALA* 3.5 35.4 - - + -
150C VAL* 3.6 17.7 - - + -
215C LEU* 4.9 2.4 - - + +
396C SER* 3.2 8.7 + - - +
397C LEU* 1.3 79.8 - - - +
399C LEU* 1.4 73.2 + - + +
401C ALA* 3.3 1.9 - - - +
402C ALA* 2.6 38.5 + - + +
431C PHE* 3.6 32.8 - + + -
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Residues in contact with LEU 399 (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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396C SER* 3.3 26.2 + - - +
398C PHE* 1.4 89.4 - - + +
400C VAL* 1.3 53.5 + - - +
402C ALA* 2.9 7.1 + - - +
403C HIS* 2.7 36.4 + - - +
420C LEU* 4.0 7.3 - - + +
425C TYR* 4.7 10.3 - - + -
426C THR 4.2 10.1 - - - +
427C TYR* 4.0 12.6 - - + -
428C THR* 4.0 27.4 - - - +
431C PHE* 3.4 49.8 - - + -
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Residues in contact with VAL 400 (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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102C CYS* 6.4 0.9 - - + -
191C LEU* 4.2 11.4 - - + -
192C ALA* 3.8 28.7 - - + -
207C PHE* 4.3 2.2 - - + -
213C TRP* 3.6 29.4 - - + -
395C TYR* 4.1 5.6 - - + -
396C SER 3.0 15.1 + - - +
399C LEU* 1.3 76.8 - - - +
401C ALA* 1.3 62.4 + - - +
403C HIS* 3.3 7.6 + - + +
404C GLN* 3.0 34.5 + - - +
425C TYR* 4.0 24.9 - - + -
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Residues in contact with ALA 401 (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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144C PHE* 3.7 29.8 - - + -
147C ALA* 3.7 13.0 - - + -
207C PHE* 3.8 14.1 - - + -
397C LEU 2.7 25.9 + - - +
398C PHE* 3.3 3.4 - - - +
400C VAL* 1.3 72.6 - - - +
402C ALA* 1.3 65.9 + - - +
404C GLN* 3.1 1.4 + - - +
405C PHE* 2.8 35.5 + - + -
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Residues in contact with ALA 402 (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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147C ALA* 3.4 26.0 - - + +
150C VAL* 4.9 2.5 - - + -
151C TRP* 3.1 23.4 + - - +
398C PHE* 2.6 27.0 + - + +
399C LEU* 3.1 14.6 - - - +
401C ALA* 1.3 75.1 - - - +
403C HIS* 1.3 65.9 + - - +
405C PHE* 3.3 1.1 + - - +
406C GLY 3.1 2.8 + - - -
420C LEU* 3.8 21.5 - - + -
431C PHE* 4.8 3.1 - - + -
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Residues in contact with HIS 403 (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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102C CYS* 3.7 15.5 - - + +
399C LEU 2.7 15.8 + - - +
400C VAL* 3.4 13.5 - - - +
402C ALA* 1.3 71.8 - - - +
404C GLN* 1.3 61.2 + - - +
406C GLY* 2.7 28.1 + - - -
407C HIS* 3.4 7.8 + + - -
413C HIS* 3.3 9.8 + - - -
420C LEU* 3.5 22.4 + - + +
421C MET* 3.2 26.2 + - + +
422C ALA 3.0 27.4 + - - -
423C PRO* 4.0 2.8 + - + -
425C TYR* 6.3 0.6 - - - -
997C ZN 2.4 34.5 - - - -
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Residues in contact with GLN 404 (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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102C CYS* 3.9 23.1 - - - +
104C ASN* 4.3 2.8 + - - -
192C ALA* 3.5 32.1 - - + +
193C HIS* 3.1 28.1 - - - +
194C ALA* 3.2 14.8 + - + +
205C SER* 4.2 11.9 - - - -
207C PHE* 4.1 11.7 - - + -
400C VAL* 3.0 24.5 + - - +
401C ALA 3.6 4.0 - - - +
403C HIS* 1.3 83.6 + - - +
405C PHE* 1.3 59.9 + - + +
407C HIS* 2.8 26.0 + - - +
408C ALA* 2.9 11.6 + - - +
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Residues in contact with PHE 405 (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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144C PHE* 3.4 25.8 - + - -
147C ALA* 3.7 19.5 - - + -
148C PHE* 3.2 63.3 - + + -
151C TRP* 4.0 13.9 - - + -
169C ILE* 4.5 2.5 - - + -
171C ILE* 3.5 20.0 - - + -
205C SER* 3.6 27.8 - - - -
207C PHE* 4.8 2.7 - + - -
401C ALA* 2.8 27.8 + - + +
402C ALA 3.8 3.8 - - - +
404C GLN* 1.3 71.6 - - - +
406C GLY* 1.3 62.3 + - - +
408C ALA* 3.1 7.0 + - + +
409C MET* 3.0 30.4 + - + +
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Residues in contact with GLY 406 (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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151C TRP* 3.5 23.3 - - - +
402C ALA 3.1 5.7 + - - -
403C HIS 2.7 13.9 + - - -
405C PHE* 1.3 77.4 - - - +
407C HIS* 1.3 58.6 + - - -
409C MET* 3.2 9.1 + - - +
410C GLY 3.4 0.7 + - - -
411C LEU* 3.1 26.4 + - - +
421C MET* 3.5 14.6 - - - -
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Residues in contact with HIS 407 (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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104C ASN* 3.5 26.2 + - + +
105C PRO 5.4 1.3 - - - -
194C ALA* 4.2 14.8 - - + +
195C PHE 4.3 2.9 - - - +
196C ALA* 3.6 6.8 - - + +
197C PRO* 3.3 9.4 - - - +
403C HIS* 3.4 13.9 + + - -
404C GLN* 2.8 13.0 + - - +
406C GLY* 1.3 71.2 - - - +
408C ALA* 1.3 57.2 + - - +
409C MET 2.9 5.6 - - - -
410C GLY* 2.7 22.2 + - - -
411C LEU 3.1 24.7 + - - +
412C GLU* 3.9 22.3 + - + -
413C HIS* 3.7 9.9 - + - -
421C MET* 3.4 18.7 - - + +
997C ZN 2.5 34.9 - - - -
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Residues in contact with ALA 408 (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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119C TRP* 2.6 33.9 + - - -
169C ILE* 3.5 26.2 - - + -
194C ALA* 4.6 1.1 - - + +
195C PHE 3.7 13.9 + - - -
197C PRO* 3.0 8.7 - - - +
203C GLY* 3.5 15.5 - - - +
205C SER* 4.2 4.0 - - - +
404C GLN 2.9 11.5 + - - +
405C PHE* 3.2 16.6 - - - +
407C HIS* 1.3 75.8 - - - +
409C MET* 1.3 50.5 + - - +
410C GLY 3.5 0.2 - - - -
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Residues in contact with MET 409 (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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118C LYS* 4.1 4.0 - - - -
119C TRP* 3.0 36.6 - - + -
124C ILE* 4.3 0.4 - - + -
151C TRP* 5.0 5.8 - - + -
157C LEU* 3.4 32.5 - - + -
159C PHE* 3.8 29.2 - - + -
169C ILE* 4.3 7.9 - - - -
197C PRO* 3.2 10.3 - - - +
405C PHE* 3.0 18.8 + - + +
406C GLY* 3.6 8.1 - - - +
407C HIS 2.9 1.2 - - - -
408C ALA* 1.3 80.2 - - - +
410C GLY* 1.3 55.7 + - - +
411C LEU* 3.7 0.7 - - - -
441C ILE* 3.9 22.4 - - + -
444C LEU* 4.4 1.0 - - - +
445C TYR* 2.2 42.3 + - + +
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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