Contacts of the strand formed by residues 415 - 422 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406F ILE* 4.2 11.2 - - + -
407F LEU 3.8 5.4 - - - +
413F ASP 3.4 0.2 + - - -
414F ARG* 1.3 84.2 + - - +
416F LEU* 1.3 61.5 + - - +
417F GLY 3.9 21.8 - - - +
418F ALA* 5.0 3.6 - - + +
435F ALA* 5.7 2.5 - - + -
436F LEU* 3.2 29.1 - - + +
440F ALA* 2.8 23.7 + - + +
441F SER 3.6 0.2 - - - -
442F CYS* 3.5 21.5 - - - +
445F ILE* 3.5 31.4 - - + -
459F PHE* 6.2 0.9 - - + -
463F ASN* 3.6 7.6 - - - +
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Residues in contact with LEU 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F ASN* 4.7 3.1 + - - -
368F GLY* 3.4 6.9 - - - -
369F LYS* 2.9 25.7 + - + +
374F LEU* 4.2 25.6 - - + -
379F ILE* 3.6 27.6 - - + -
381F TYR* 4.4 0.9 - - + -
407F LEU 2.7 14.7 + - - +
408F GLY 3.9 2.9 - - - -
409F GLN* 3.3 36.8 - - + +
414F ARG* 3.4 24.9 - - + +
415F VAL* 1.3 78.8 - - - +
417F GLY* 1.3 55.5 + - - +
436F LEU* 4.4 6.7 - - - +
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Residues in contact with GLY 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F VAL 3.5 10.5 - - - -
368F GLY* 4.1 0.2 - - - -
369F LYS 3.5 18.2 - - - -
406F ILE* 3.6 2.3 - - - -
407F LEU* 2.9 32.1 + - - +
415F VAL* 3.7 8.7 - - - +
416F LEU* 1.3 81.1 - - - +
418F ALA* 1.3 60.6 + - - +
419F HIS* 4.0 6.3 - - - -
436F LEU* 5.2 1.8 - - - -
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Residues in contact with ALA 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F ALA 4.7 0.2 - - - -
366F TRP* 3.2 5.4 - - - +
367F VAL* 3.0 35.3 + - + +
405F LYS 3.5 5.2 - - - -
406F ILE* 3.6 20.0 - - + -
415F VAL* 5.0 4.7 - - + -
417F GLY* 1.3 75.0 - - - -
419F HIS* 1.3 62.7 + - - +
420F ILE* 4.9 5.4 - - + -
429F VAL* 5.1 0.5 - - - +
432F ALA* 3.8 30.1 - - + -
436F LEU* 5.6 1.3 - - + +
459F PHE* 4.1 4.0 - - + -
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Residues in contact with HIS 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F ASP* 3.6 21.2 + - + +
222F ILE* 3.7 24.3 - - + +
365F ALA 3.6 3.4 - - - -
366F TRP* 3.3 32.7 - + + +
367F VAL 4.9 1.8 - - - -
368F GLY 4.9 0.2 - - - -
369F LYS 2.7 32.4 + - - -
370F SER* 3.6 19.6 - - - -
403F MET 4.0 1.0 - - - +
404F VAL* 3.5 1.7 - - - +
405F LYS* 2.7 53.7 + - + +
406F ILE* 4.9 0.4 - - - +
407F LEU* 3.9 11.6 - - + +
417F GLY 4.0 2.5 - - - -
418F ALA* 1.3 83.6 + - - +
420F ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ILE* 4.7 2.0 - - - +
364F VAL* 3.2 8.6 - - - +
365F ALA 2.7 41.4 + - - +
388F PHE* 4.1 24.2 - - + -
403F MET 3.7 1.8 - - - -
404F VAL* 4.1 15.5 - - + -
418F ALA* 4.9 2.2 - - + +
419F HIS* 1.3 82.5 - - - +
421F LEU* 1.3 62.1 + - - +
422F GLY 4.1 0.2 - - - -
425F ALA* 3.5 28.9 - - + +
428F MET* 4.0 19.5 - - + -
429F VAL* 3.7 41.3 - - + +
432F ALA* 5.2 4.0 - - + -
459F PHE* 5.1 6.7 - - + -
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Residues in contact with LEU 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ILE* 4.1 22.9 - - + +
225F ASN* 3.7 32.3 - - + +
226F PHE* 3.9 20.0 - - + +
229F ILE* 4.0 12.8 - - + -
362F PRO* 3.9 17.0 - - + -
363F GLU 3.5 13.0 - - - +
364F VAL* 3.8 17.0 - - + -
388F PHE* 3.4 4.4 - - - -
402F GLY* 3.0 15.6 - - - -
403F MET* 2.7 46.0 + - + +
419F HIS 4.3 0.2 - - - -
420F ILE* 1.3 73.2 - - - +
422F GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362F PRO* 3.5 18.6 - - - -
363F GLU 2.9 25.9 + - - +
388F PHE* 3.9 4.9 - - - -
401F ASP 3.5 4.9 - - - -
420F ILE 4.1 1.0 - - - -
421F LEU* 1.3 75.4 - - - +
423F PRO* 1.3 78.7 - - - +
424F GLY 3.4 1.9 + - - -
425F ALA* 3.4 8.9 + - - +
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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