Contacts of the strand formed by residues 415 - 422 (chain B) in PDB entry 1ZMC
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406B ILE* 4.6 8.7 - - + -
407B LEU 3.7 5.2 - - - +
414B ARG* 1.3 77.9 + - - +
416B LEU* 1.3 60.1 + - - +
417B GLY 4.0 18.8 - - - +
418B ALA* 4.9 6.7 - - + +
432B ALA* 6.2 0.9 - - + -
435B ALA* 5.4 2.9 - - + -
436B LEU* 3.2 33.9 - - + +
440B ALA* 3.0 19.7 + - + +
441B SER 3.6 4.7 - - - +
442B CYS* 3.6 23.6 - - - +
445B ILE* 3.8 12.8 - - + -
459B PHE* 6.0 1.3 - - + -
463B ASN* 3.7 16.4 - - - +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ASN* 5.0 2.8 + - - -
368B GLY* 3.6 6.4 - - - -
369B LYS* 3.0 25.6 + - + +
374B LEU* 4.0 24.9 - - + -
379B ILE* 3.7 25.4 - - + -
381B TYR* 4.6 0.7 - - + -
407B LEU 2.7 15.1 + - - +
408B GLY 4.1 2.2 - - - -
409B GLN* 3.6 44.9 - - + +
414B ARG* 3.6 24.7 - - + +
415B VAL* 1.3 75.4 - - - +
417B GLY* 1.3 54.7 + - - +
436B LEU* 4.5 5.8 - - - +
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B VAL 3.6 9.4 - - - -
369B LYS 3.6 18.4 - - - -
405B LYS 4.1 0.3 - - - +
406B ILE* 3.7 2.4 - - - -
407B LEU* 3.0 32.3 + - - +
415B VAL* 3.5 8.9 - - - +
416B LEU* 1.3 81.8 - - - +
418B ALA* 1.3 60.6 + - - +
419B HIS* 4.1 6.3 - - - -
436B LEU* 5.3 0.9 - - - -
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B ALA 4.6 0.2 - - - -
366B TRP* 3.2 7.6 - - - +
367B VAL* 3.0 34.3 + - + +
405B LYS 3.7 3.6 - - - -
406B ILE* 3.9 16.4 - - + -
415B VAL* 5.0 5.8 - - + -
417B GLY* 1.3 73.0 - - - +
419B HIS* 1.3 63.5 + - - +
420B ILE* 5.1 4.5 - - + -
429B VAL* 5.9 0.7 - - + -
432B ALA* 3.6 31.0 - - + -
436B LEU* 5.7 0.8 - - + +
459B PHE* 4.0 5.8 - - + -
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Residues in contact with HIS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLY 5.0 0.2 - - - -
218B ILE* 6.1 0.2 - - - +
219B ASP* 3.5 29.3 + - + +
222B ILE* 3.8 24.6 - - + +
365B ALA 3.6 4.3 - - - -
366B TRP* 3.4 32.2 - + + +
367B VAL 5.2 1.8 - - - -
369B LYS 2.9 29.7 + - - -
370B SER* 3.8 9.2 - - - -
403B MET 4.0 0.7 - - - +
404B VAL* 3.5 2.6 - - - +
405B LYS* 2.6 55.9 + - + +
406B ILE* 5.0 0.6 - - - +
407B LEU* 3.7 17.6 - - + +
418B ALA* 1.3 82.7 + - - +
420B ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE* 4.8 2.7 - - - +
363B GLU 3.8 0.5 - - - +
364B VAL* 3.3 8.5 - - - +
365B ALA 2.9 42.0 + - - +
388B PHE* 3.9 28.9 - - + -
403B MET 3.7 2.0 - - - -
404B VAL* 4.1 11.9 - - + -
418B ALA* 5.1 3.6 - - + -
419B HIS* 1.3 81.7 - - - +
421B LEU* 1.3 62.1 + - - +
422B GLY 4.6 0.2 - - - +
425B ALA* 3.7 25.9 - - + +
428B MET* 3.7 38.4 - - + +
429B VAL* 3.9 19.3 - - + +
432B ALA* 5.6 0.2 - - + -
459B PHE* 4.7 9.4 - - + -
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE* 4.0 21.9 - - + +
225B ASN* 3.6 34.5 - - + +
226B PHE* 3.7 40.6 - - + +
229B ILE* 4.0 11.2 - - + -
362B PRO* 4.0 11.7 - - + -
363B GLU 3.6 10.1 - - - +
364B VAL* 4.0 6.3 - - + -
388B PHE* 3.5 3.8 - - - -
402B GLY* 3.0 13.2 - - - -
403B MET* 2.7 44.0 + - + +
419B HIS 4.3 0.2 - - - -
420B ILE* 1.3 73.4 - - - +
422B GLY* 1.3 58.7 - - - +
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Residues in contact with GLY 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B PRO* 3.7 14.0 - - - +
363B GLU* 2.9 35.7 + - - +
388B PHE* 3.9 3.8 - - - -
401B ASP 3.6 8.1 - - - -
420B ILE 4.0 1.0 - - - -
421B LEU* 1.3 75.1 - - - +
423B PRO* 1.3 77.0 - - - +
425B ALA* 3.7 4.2 + - - +
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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