Contacts of the helix formed by residues 393 - 408 (chain C) in PDB entry 1U3Q
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 GLN 393 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C TRP* 3.8 1.6 - - - -
391C LYS* 3.1 24.0 + - - +
392C LEU* 1.3 77.0 + - - +
394C HIS* 1.3 65.1 + - - +
395C LYS* 4.3 6.7 - - + +
396C GLU* 2.8 34.7 + - + +
397C TYR* 3.0 22.2 + - - +
440C VAL* 5.6 2.0 - - + -
444C SER* 6.4 2.5 - - - -
454C ARG* 4.7 3.1 - - - +
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Residues in contact with HIS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 3.2 35.7 - - + +
276C GLU* 4.7 5.7 - - - +
345C TRP* 3.4 43.2 - + + -
393C GLN* 1.3 74.2 + - - +
395C LYS* 1.3 64.0 + - + +
397C TYR* 3.4 9.4 + + - +
398C LEU* 3.1 48.3 + - + +
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Residues in contact with LYS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C GLU* 5.9 0.4 + - - -
269C VAL* 3.9 24.5 - - + +
270C LEU* 5.6 8.5 - - - +
273C LEU* 5.8 7.9 - - - -
393C GLN* 3.2 3.6 - - + +
394C HIS* 1.3 82.2 - - + +
396C GLU* 1.3 64.6 + - + +
398C LEU* 3.7 11.1 + - + +
399C CYS* 3.3 28.1 + - - -
439C TRP* 5.3 11.5 - - + -
440C VAL* 3.6 28.0 - - + +
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LEU* 3.7 10.9 - - + +
393C GLN* 2.8 42.9 + - + +
395C LYS* 1.3 74.3 - - - +
397C TYR* 1.3 56.1 + - - +
399C CYS* 3.1 2.3 + - - +
400C VAL* 2.6 40.9 + - - +
437C LEU* 4.1 21.7 - - + +
440C VAL* 3.9 18.3 - - + +
441C ILE* 3.7 13.0 - - + +
454C ARG* 2.7 42.7 + - - -
458C LEU* 4.1 9.1 - - + +
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Residues in contact with TYR 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 3.6 13.9 + - - -
341C MET* 3.6 27.4 - - + -
342C GLY* 3.7 15.6 - - - -
345C TRP* 3.5 59.6 - + + -
392C LEU* 4.0 10.0 - - + +
393C GLN 3.0 12.7 + - - +
394C HIS* 3.5 16.6 - + - +
396C GLU* 1.3 78.3 - - - +
398C LEU* 1.3 62.6 + - + +
400C VAL* 3.8 6.0 - - - +
401C LYS* 2.8 77.6 + - + +
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 4.4 9.6 - - + +
272C LEU* 3.6 22.3 - - + +
273C LEU* 3.7 30.1 - - + +
276C GLU* 3.5 42.0 - - + +
312C TRP* 5.1 1.7 + - - -
394C HIS* 3.1 39.1 + - + +
395C LYS* 3.8 13.0 - - + +
396C GLU 3.2 0.2 - - - -
397C TYR* 1.3 91.1 - - + +
399C CYS* 1.3 61.8 + - - +
401C LYS* 3.8 5.2 - - - +
402C ALA* 3.3 22.2 + - - +
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Residues in contact with CYS 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 3.9 26.2 - - - -
272C LEU* 4.1 13.0 - - - -
395C LYS 3.3 15.0 + - - +
396C GLU* 3.1 7.9 + - - +
398C LEU* 1.3 77.6 - - - +
400C VAL* 1.3 65.5 + - - +
402C ALA* 3.2 4.7 + - - +
403C MET* 3.1 26.7 + - - +
433C VAL* 3.7 6.9 - - + +
436C ALA* 3.9 9.2 - - - -
437C LEU* 3.9 39.0 - - + +
440C VAL* 4.3 1.8 - - - -
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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
----------------------------------------------------------
341C MET* 4.0 25.4 - - + -
387C PHE* 5.2 7.4 - - + -
392C LEU* 5.2 2.9 - - + -
396C GLU 2.6 25.9 + - - +
397C TYR* 3.8 6.5 - - - +
399C CYS* 1.3 73.2 - - - +
401C LYS* 1.3 62.2 + - - +
403C MET* 3.2 10.5 + - - +
404C ILE* 3.1 22.6 + - + +
437C LEU* 4.4 18.8 - - + -
458C LEU* 4.5 24.7 - - + +
459C LEU* 5.3 4.9 - - + -
462C LEU* 4.0 22.4 - - + +
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Residues in contact with LYS 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 2.7 38.9 + - - -
277C PRO* 3.5 16.8 - - - +
312C TRP* 3.5 26.1 - - + -
338C VAL* 3.9 32.5 - - + +
341C MET* 4.0 22.0 - - + -
342C GLY* 5.3 1.6 - - - +
397C TYR* 2.8 49.6 + - + +
398C LEU* 3.8 6.5 - - - +
400C VAL* 1.3 75.5 - - - +
402C ALA* 1.3 60.4 + - - +
403C MET 3.3 0.5 + - - -
404C ILE* 3.3 18.6 + - + +
405C LEU 3.5 5.4 + - - -
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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
----------------------------------------------------------
272C LEU* 4.1 22.0 - - + -
312C TRP* 3.8 15.9 - - + -
316C ILE* 4.4 8.9 - - + +
398C LEU 3.3 14.3 + - - +
399C CYS 3.2 5.9 + - - +
401C LYS* 1.3 78.1 - - - +
403C MET* 1.3 60.5 + - - +
405C LEU* 3.5 3.5 + - - +
406C LEU* 3.3 28.8 + - - +
433C VAL* 4.1 17.3 - - + -
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Residues in contact with MET 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ALA* 5.6 0.4 - - + -
460A MET* 3.5 32.1 - - + -
399C CYS 3.1 11.1 + - - +
400C VAL* 3.5 11.9 - - - +
401C LYS 3.2 0.4 - - - -
402C ALA* 1.3 73.3 - - - +
404C ILE* 1.3 66.9 + - - +
405C LEU 3.1 2.0 - - - -
407C ASN* 2.9 30.4 + - - +
430C LEU* 4.2 17.0 - - + -
433C VAL* 3.5 24.7 - - + -
434C THR* 4.6 14.8 - - - +
437C LEU* 4.1 23.6 - - - -
459C LEU* 3.3 30.1 - - + -
462C LEU* 4.0 10.8 - - + -
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Residues in contact with ILE 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C CYS* 4.3 2.0 - - + -
337C GLU* 3.4 40.2 - - + +
338C VAL* 4.1 12.8 - - + +
341C MET* 3.9 36.1 - - + -
400C VAL 3.1 14.6 + - - +
401C LYS* 3.3 10.1 + - - +
403C MET* 1.3 76.0 - - - +
405C LEU* 1.3 57.3 + - - +
407C ASN* 5.1 1.8 - - - -
408C SER* 3.0 33.6 + - - -
462C LEU* 3.5 28.0 - - + +
465C VAL* 4.1 14.8 - - + -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C TRP* 3.7 25.4 - - + -
313C ALA* 3.8 16.6 - - + -
316C ILE* 3.6 29.6 - - + -
319C PHE* 4.4 13.5 - - + -
330C LEU* 3.7 20.0 - - + +
331C LEU* 3.9 19.7 - - + -
334C CYS* 3.1 35.9 - - - -
338C VAL* 4.7 0.8 - - + +
401C LYS 3.5 1.8 + - - -
402C ALA 3.6 8.1 - - - +
403C MET 3.1 0.6 - - - -
404C ILE* 1.3 78.8 - - - +
406C LEU* 1.3 64.5 + - + +
408C SER* 2.8 21.8 + - - -
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Residues in contact with LEU 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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316C ILE* 4.9 9.2 - - + -
319C PHE* 4.5 20.0 - - + -
322C LEU* 5.1 0.4 - - + -
330C LEU* 4.0 8.5 - - + +
402C ALA 3.3 14.4 + - - +
405C LEU* 1.3 84.5 - - + +
407C ASN* 1.3 58.2 + - - +
408C SER 3.5 0.2 - - - -
409C SER 5.0 1.2 + - - +
426C LEU* 3.6 43.6 - - + +
429C LEU* 3.7 41.3 - - + +
430C LEU* 3.5 21.9 - - + +
433C VAL* 3.6 31.2 - - + -
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Residues in contact with ASN 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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386A ARG* 5.1 9.9 - - - +
460A MET* 3.4 35.2 - - - +
461A LEU* 6.0 1.6 - - - +
463A SER* 4.8 3.8 - - - -
464A HIS* 2.8 54.7 + - - -
403C MET 2.9 17.5 + - - +
404C ILE* 3.8 2.0 - - - +
406C LEU* 1.3 76.5 - - - +
408C SER* 1.3 59.5 + - - +
409C SER 3.3 5.5 + - - -
430C LEU* 3.4 26.5 - - + +
462C LEU* 5.6 3.7 - - + +
466C ARG* 3.9 2.0 + - - -
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Residues in contact with SER 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A HIS* 4.1 2.1 + - - -
467A HIS* 5.8 0.9 - - - -
330C LEU* 3.0 19.9 + - - -
333C SER* 3.0 19.8 + - - -
334C CYS* 3.2 20.2 - - - -
337C GLU* 4.7 3.1 - - - -
404C ILE 3.0 19.8 + - - -
405C LEU 2.8 16.0 + - - -
407C ASN* 1.3 78.4 - - - +
409C SER* 1.3 61.4 + - - +
410C MET* 3.8 4.5 + - - +
466C ARG* 3.4 26.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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