Contacts of the helix formed by residues 420 - 434 (chain C) in PDB entry 5UH8
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 ILE 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C PHE* 3.2 34.3 - - + +
154C MET* 3.8 24.0 - - + +
155C GLY* 3.8 20.9 - - - +
396C MET* 4.9 0.2 - - - -
418C ILE* 3.6 22.6 + - + -
419C ASN* 1.3 72.2 + - - +
421C ARG* 1.3 60.9 + - - +
422C PRO 3.3 2.0 - - - -
423C VAL* 2.9 24.8 + - + +
424C VAL* 3.1 18.9 + - + +
387F LEU* 3.7 35.0 - - + -
388F GLN* 4.3 11.3 - - - +
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Residues in contact with ARG 421 (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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403C ARG* 5.4 4.2 - - - +
419C ASN* 3.3 28.9 + - - +
420C ILE* 1.3 81.4 - - - +
422C PRO* 1.3 69.5 - - + +
424C VAL* 3.7 5.1 + - - +
425C ALA* 3.1 28.5 + - + +
380F GLY* 3.6 32.6 + - - -
383F GLN* 4.8 15.5 + - - +
384F ARG* 4.4 12.1 - - - +
387F LEU* 5.5 5.1 - - - +
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Residues in contact with PRO 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C GLY* 4.0 7.1 - - - +
395C ARG* 3.9 34.1 + - + -
396C MET* 4.4 12.6 - - + +
399C VAL* 5.0 6.5 - - + -
419C ASN* 3.1 28.7 - - - +
421C ARG* 1.3 95.6 - - + +
423C VAL* 1.3 59.1 + - - +
425C ALA* 3.9 5.6 - - + +
426C ALA* 3.2 25.1 + - - +
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 6.5 0.7 - - + -
154C MET* 3.8 30.7 - - + +
389C ILE* 5.6 4.5 - - + +
392C GLY* 4.3 14.6 - - - +
393C MET* 3.9 28.0 - - - -
396C MET* 4.0 20.2 - - + -
420C ILE* 2.9 15.2 + - - +
422C PRO* 1.3 76.2 - - - +
424C VAL* 1.3 65.9 + - - +
426C ALA* 3.2 12.0 + - - +
427C ILE* 3.2 23.3 + - + +
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Residues in contact with VAL 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C MET 3.9 19.5 - - - +
155C GLY* 4.1 11.7 - - - -
156C ASP 5.0 8.3 - - - +
420C ILE* 3.1 22.6 + - + +
421C ARG* 4.4 4.5 - - - +
423C VAL* 1.3 75.5 - - - +
425C ALA* 1.3 57.2 + - - +
427C ILE* 3.2 18.9 - - + +
428C LYS* 3.0 36.4 + - + +
393F GLU* 4.5 15.9 - - - +
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ARG* 6.3 0.4 - - - +
421C ARG* 3.1 22.6 + - + +
422C PRO* 4.0 6.7 - - + +
424C VAL* 1.3 78.3 - - - +
426C ALA* 1.3 58.8 + - - +
428C LYS* 4.1 6.6 - - - +
429C GLU* 3.2 30.0 + - - +
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLN* 2.9 40.9 - - - +
389C ILE* 5.9 0.2 - - - -
391C VAL* 5.2 0.9 - - + -
392C GLY* 3.9 20.4 - - - +
395C ARG* 4.1 14.6 - - - +
422C PRO 3.2 17.9 + - - +
423C VAL 3.2 5.6 + - - +
425C ALA* 1.3 77.1 - - - +
427C ILE* 1.3 63.4 + - + +
429C GLU* 4.3 8.0 - - - +
430C PHE* 4.0 7.8 + - - +
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Residues in contact with ILE 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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156C ASP 4.1 16.4 - - - +
157C PHE* 5.2 11.7 - - + -
158C PRO* 4.2 17.3 - - + -
385C ILE* 5.5 4.9 - - + -
388C GLN* 5.6 2.2 - - + -
389C ILE* 4.1 32.1 - - + +
423C VAL* 3.2 21.0 + - + +
424C VAL* 3.2 31.0 - - + +
426C ALA* 1.3 79.7 - - - +
428C LYS* 1.3 80.7 + - + +
429C GLU 3.3 0.4 - - - -
430C PHE* 3.6 5.0 + - - +
431C PHE* 3.1 36.5 + - + -
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Residues in contact with LYS 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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158C PRO* 6.4 0.2 - - - -
168C ILE* 6.0 0.3 - - - +
169C ASN* 6.0 4.5 - - - +
424C VAL* 3.0 22.8 + - + +
425C ALA* 4.1 6.1 - - - +
427C ILE* 1.3 83.9 - - + +
429C GLU* 1.3 63.5 + - - +
431C PHE* 3.4 7.7 + - - +
432C GLY* 3.2 17.5 + - - -
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Residues in contact with GLU 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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388C GLN* 4.3 12.1 - - - +
395C ARG* 5.3 6.9 + - - -
425C ALA 3.2 17.8 + - - +
426C ALA* 4.6 5.3 - - - +
428C LYS* 1.3 82.1 - - - +
430C PHE* 1.3 57.1 + - - +
432C GLY* 4.5 0.7 - - - +
433C THR* 2.8 51.2 + - - +
395D GLY* 5.4 8.3 - - - -
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Residues in contact with PHE 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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175C VAL* 4.3 26.5 - - + -
384C LEU* 4.0 38.4 - - + -
385C ILE* 4.4 18.4 - - + -
388C GLN* 3.5 36.3 + - + -
426C ALA 4.0 6.3 + - - +
427C ILE* 3.6 9.5 + - - +
428C LYS 3.3 0.6 - - - -
429C GLU* 1.3 81.1 - - - +
431C PHE* 1.3 79.2 + + - +
432C GLY 3.3 0.7 + - - -
434C SER* 3.3 47.1 + - - -
436C LEU* 4.8 9.2 - - + -
437C SER* 3.6 9.4 - - - -
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Residues in contact with PHE 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PRO* 3.6 37.0 - - + -
166C PHE* 3.9 30.5 - + + -
168C ILE* 3.6 34.3 - - + +
173C ARG* 3.6 16.1 + - + -
175C VAL* 4.2 14.4 - - + -
385C ILE* 4.2 27.6 - - + -
427C ILE* 3.1 27.1 + - + -
428C LYS* 3.4 8.5 + - - +
429C GLU 3.3 0.2 - - - -
430C PHE* 1.3 92.8 - + - +
432C GLY* 1.3 57.9 + - - +
437C SER* 2.6 29.2 + - - -
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Residues in contact with GLY 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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168C ILE* 5.5 4.7 - - - -
173C ARG* 5.3 9.0 + - - -
428C LYS 3.2 9.9 + - - -
429C GLU* 3.2 5.4 + - - -
431C PHE* 1.3 79.4 - - - +
433C THR* 1.3 62.9 + - - +
437C SER* 5.7 0.9 - - - -
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Residues in contact with THR 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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429C GLU* 2.8 34.1 + - + +
431C PHE 3.7 0.4 - - - -
432C GLY* 1.3 82.8 + - - +
434C SER* 1.3 69.5 + - - +
435C GLN* 3.7 3.5 + - - +
428F GLY* 5.7 4.2 - - - -
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Residues in contact with SER 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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429C GLU 3.9 0.6 + - - -
430C PHE* 3.3 47.2 + - - -
432C GLY 5.4 0.2 - - - -
433C THR* 1.3 85.9 - - - +
435C GLN* 1.3 59.6 + - - +
436C LEU* 3.1 15.6 + - - +
437C SER* 3.5 17.1 + - - +
460C PRO* 4.2 19.0 - - - +
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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