Contacts of the strand formed by residues 415 - 422 (chain C) in PDB entry 1ZMD
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 415 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406C ILE* 4.3 9.0 - - + -
407C LEU 3.8 5.6 - - - +
413C ASP 3.4 0.4 + - - -
414C ARG* 1.3 81.8 + - - +
416C LEU* 1.3 62.2 + - - +
417C GLY 3.9 19.7 - - - +
418C ALA* 4.8 6.1 - - + +
435C ALA* 5.1 3.4 - - + -
436C LEU* 3.6 34.1 - - + +
439C GLY* 6.0 0.3 - - - -
440C ALA 3.0 21.5 + - - +
441C SER 3.6 17.7 - - - -
442C CYS* 3.6 7.9 - - - +
445C ILE* 3.7 24.5 - - + -
459C PHE* 6.1 0.4 - - + -
463C ASN* 3.7 6.3 - - - +
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Residues in contact with LEU 416 (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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352C ASN* 5.0 2.8 + - - -
368C GLY* 3.4 7.9 - - - -
369C LYS* 2.9 26.9 + - + +
374C LEU* 3.8 25.6 - - + -
379C ILE* 3.7 27.6 - - + -
381C TYR* 4.5 0.9 - - + -
407C LEU* 2.7 10.7 + - - +
408C GLY 4.1 3.8 - - - +
409C GLN* 3.7 43.5 - - + +
414C ARG* 3.6 21.1 - - + +
415C VAL* 1.3 77.9 - - - +
417C GLY* 1.3 58.6 + - - +
436C LEU* 4.5 5.0 - - - +
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Residues in contact with GLY 417 (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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367C VAL 3.6 6.3 - - - -
369C LYS 3.6 19.3 - - - -
405C LYS 4.0 0.3 - - - +
406C ILE* 3.5 5.9 - - - +
407C LEU* 2.8 36.8 + - - +
415C VAL* 3.6 4.8 - - - +
416C LEU* 1.3 82.0 - - - +
418C ALA* 1.3 61.2 + - - +
419C HIS* 4.0 4.9 - - - -
436C LEU* 5.3 0.9 - - - -
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Residues in contact with ALA 418 (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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366C TRP* 3.1 7.2 - - - +
367C VAL* 3.0 38.1 + - + +
405C LYS 3.8 3.6 - - - -
406C ILE* 3.9 16.4 - - + -
415C VAL* 4.8 6.7 - - + -
417C GLY* 1.3 74.1 - - - +
419C HIS* 1.3 61.5 + - - +
420C ILE* 5.1 4.0 - - + -
429C VAL* 5.2 0.4 - - + +
432C ALA* 3.6 31.0 - - + -
436C LEU* 5.5 1.1 - - + +
459C PHE* 4.0 5.4 - - + -
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Residues in contact with HIS 419 (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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219C ASP* 3.6 21.1 + - + +
222C ILE* 3.7 24.4 - - + +
365C ALA 3.6 3.8 - - - +
366C TRP* 3.2 34.1 - + + +
367C VAL 4.9 2.0 - - - -
368C GLY 4.9 0.2 - - - -
369C LYS 2.6 32.5 + - - -
370C SER* 3.5 18.4 - - - -
403C MET 3.9 0.9 - - - +
404C VAL* 3.5 2.8 - - - +
405C LYS* 2.8 55.6 + - + +
406C ILE* 4.9 0.8 - - - +
407C LEU* 3.9 12.3 - - + +
417C GLY* 4.0 3.1 - - - -
418C ALA* 1.3 82.6 + - - +
420C ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 420 (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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222C ILE* 4.8 2.6 - - - +
364C VAL* 3.1 9.2 - - - +
365C ALA 2.7 45.6 + - - +
388C PHE* 4.0 25.8 - - + -
403C MET 3.7 1.8 - - - -
404C VAL* 4.0 21.3 - - + -
418C ALA 5.2 2.0 - - - -
419C HIS* 1.3 83.8 - - - +
421C LEU* 1.3 61.8 + - - +
422C GLY 4.0 0.4 - - - -
425C ALA* 3.5 28.9 - - + +
428C MET* 4.0 16.4 - - + +
429C VAL* 3.9 34.5 - - + +
432C ALA* 5.2 0.9 - - + -
459C PHE* 4.8 9.2 - - + -
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Residues in contact with LEU 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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222C ILE* 4.0 20.6 - - + +
225C ASN* 3.3 36.6 - - + +
226C PHE* 3.6 42.0 - - + +
229C ILE* 4.0 11.7 - - + -
362C PRO* 3.9 15.7 - - + -
363C GLU 3.6 6.5 - - - +
364C VAL* 3.9 6.1 - - + -
388C PHE* 3.4 3.8 - - - -
402C GLY* 3.2 14.7 - - - -
403C MET* 2.8 41.7 + - + +
419C HIS 4.3 0.2 - - - -
420C ILE* 1.3 72.3 - - - +
422C GLY* 1.3 57.8 - - - +
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Residues in contact with GLY 422 (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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362C PRO* 3.6 16.4 - - - +
363C GLU 2.9 26.1 + - - +
388C PHE* 3.7 4.9 - - - -
401C ASP 3.6 7.9 - - - -
420C ILE 4.0 1.2 - - - -
421C LEU* 1.3 75.5 - - - +
423C PRO* 1.3 78.2 - - - +
424C GLY 3.6 0.2 + - - -
425C ALA* 3.5 10.3 + - - -
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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