Contacts of the helix formed by residues 395 - 404 (chain C) in PDB entry 3E20
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 SER 395 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277C TYR* 5.3 6.0 - - - -
280C GLU* 3.7 16.3 + - - +
281C LYS* 3.4 36.9 - - - +
392C SER 4.0 0.4 + - - -
394C ARG* 1.3 83.9 - - - +
396C GLN* 1.3 66.2 + - - +
397C GLU* 3.9 2.7 + - - +
398C GLY* 2.9 23.4 + - - -
399C MET* 3.0 22.7 + - - +
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Residues in contact with GLN 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LYS* 5.3 3.4 - - - +
395C SER* 1.3 74.1 - - - +
397C GLU* 1.3 75.1 + - - +
399C MET* 3.4 6.0 + - - +
400C GLN* 3.0 32.2 + - + +
577D TYR* 3.2 32.4 - - + -
578D SER* 2.8 39.5 - - - +
647D ASP* 3.3 28.8 + - - +
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Residues in contact with GLU 397 (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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281C LYS* 3.0 56.1 + - - +
284C ILE* 3.7 23.1 - - + +
285C GLN* 3.5 33.4 - - + +
288C PHE* 4.1 11.9 - - + -
395C SER* 3.9 4.0 - - - +
396C GLN* 1.3 87.3 + - - +
398C GLY* 1.3 52.4 + - - +
400C GLN* 3.0 11.5 + - - +
401C PHE* 2.7 35.5 + - - +
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Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ILE* 3.6 14.1 - - - -
391C VAL* 5.6 0.9 - - - -
392C SER 3.7 15.5 - - - -
393C ASP* 4.0 2.0 - - - -
395C SER* 2.9 21.7 + - - -
397C GLU* 1.3 74.8 - - - +
399C MET* 1.3 51.7 + - - +
401C PHE* 2.9 4.1 + - - +
402C VAL* 2.7 43.8 + - - +
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Residues in contact with MET 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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393C ASP* 3.9 37.6 - - - +
395C SER 3.0 12.8 + - - +
396C GLN* 3.8 9.6 - - - +
398C GLY* 1.3 72.7 - - - +
400C GLN* 1.3 57.5 + - - +
402C VAL* 3.8 4.7 - - - +
403C LYS* 2.8 50.5 + - + +
576D GLY* 4.0 12.8 - - - +
578D SER* 5.3 9.0 - - - -
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Residues in contact with GLN 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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285C GLN* 5.6 0.5 - - - +
288C PHE* 3.8 24.9 - - + -
396C GLN* 3.0 25.3 + - - +
397C GLU* 3.2 9.2 - - - +
399C MET* 1.3 74.6 - - - +
401C PHE* 1.3 61.3 + - - +
402C VAL 2.9 0.2 + - - -
404C GLY* 2.7 35.3 + - - -
405C PHE* 3.5 3.0 + - - -
572D ILE* 4.3 6.5 - - - +
573D LEU* 4.1 3.0 - - - +
574D THR* 2.7 51.2 + - - +
576D GLY* 3.4 11.8 + - - -
577D TYR* 3.5 39.6 - - + +
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Residues in contact with PHE 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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284C ILE* 3.8 17.7 - - + -
287C PHE* 4.3 30.7 - + - -
288C PHE* 4.7 0.7 - - - -
318C LEU* 3.2 48.7 - - + -
320C PHE 4.4 0.2 - - - -
391C VAL* 3.8 29.2 - - + -
397C GLU 2.7 16.4 + - - +
398C GLY 3.4 6.1 - - - +
400C GLN* 1.3 73.7 - - - +
402C VAL* 1.3 62.3 + - + +
405C PHE* 3.5 22.9 + - + -
407C GLY* 3.0 46.4 + - - -
408C ILE 4.5 1.1 - - - -
409C GLY* 3.6 13.5 - - - -
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Residues in contact with VAL 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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320C PHE* 3.4 58.6 - - + -
391C VAL* 5.8 0.4 - - + -
392C SER 5.4 0.2 - - - -
393C ASP* 3.8 11.4 - - + +
398C GLY* 2.7 24.0 + - - +
399C MET* 3.8 8.3 - - - +
400C GLN 2.9 0.8 + - - -
401C PHE* 1.3 77.5 - - + +
403C LYS* 1.3 65.2 + - + +
404C GLY 3.2 1.6 - - - -
406C GLY* 3.4 10.5 + - - -
407C GLY* 3.3 19.7 + - - -
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Residues in contact with LYS 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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399C MET* 2.8 34.4 + - + +
402C VAL* 1.3 77.9 - - + +
404C GLY* 1.3 59.3 + - - +
406C GLY 4.8 0.9 - - - -
575D THR* 3.7 14.5 - - + +
576D GLY* 4.4 9.9 - - - -
591D SER* 5.1 9.7 + - - +
592D PHE 6.1 1.1 - - - +
624D GLU* 4.5 16.0 + - - -
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Residues in contact with GLY 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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300C PHE* 4.5 4.9 - - - -
400C GLN 2.7 20.0 + - - -
403C LYS* 1.3 76.1 - - - +
405C PHE* 1.3 73.9 + - - +
406C GLY 3.7 2.1 + - - -
574D THR 4.9 1.3 - - - -
575D THR* 3.8 24.4 - - - +
576D GLY 4.1 3.2 - - - +
611D MET* 5.5 1.4 - - - +
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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