Contacts of the strand formed by residues 450 - 455 (chain B) in PDB entry 4Z4Q
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 450 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ALA* 3.8 4.3 - - - +
428B GLU* 2.9 30.7 + - - +
430B TYR* 3.4 20.5 - - + -
445B ARG* 3.0 45.4 + - + +
446B ASP 2.9 33.1 + - - +
449B PHE* 1.3 106.2 - - + +
451B ALA* 1.3 60.2 + - - +
452B ILE* 5.3 0.2 - - + -
592B TRP* 3.7 6.8 - - - -
596B MET* 3.2 27.6 + - + +
601B ARG* 4.0 0.6 - - - +
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Residues in contact with ALA 451 (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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416B LEU* 4.8 2.2 - - + -
417B THR 3.2 17.0 - - - +
418B PRO* 4.2 1.8 - - + -
419B ALA* 3.7 14.3 - - + +
428B GLU 2.9 14.0 + - - +
429B LEU* 4.1 6.7 - - + -
430B TYR* 3.1 24.1 + - - +
449B PHE 4.1 0.6 + - - -
450B GLN* 1.3 74.2 - - - +
452B ILE* 1.3 73.3 + - - +
498B TYR* 3.9 25.6 - - + +
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Residues in contact with ILE 452 (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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416B LEU* 3.6 5.2 - - - +
417B THR* 3.0 40.4 + - - +
429B LEU* 4.6 0.2 - - - -
430B TYR* 3.6 14.1 - - + -
432B VAL* 4.1 19.1 - - + -
438B GLY* 3.9 24.7 - - - +
441B ALA* 3.8 24.7 - - + +
442B LYS* 4.0 20.4 - - + +
445B ARG* 4.1 15.5 - - + +
450B GLN 5.0 0.9 - - - +
451B ALA* 1.3 84.6 - - - +
453B LEU* 1.3 65.7 + - - +
454B PRO* 4.0 9.7 - - + +
596B MET* 4.0 11.9 - - + -
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Residues in contact with LEU 453 (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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415B LYS* 3.6 27.8 - - + +
416B LEU* 3.9 20.4 - - + -
429B LEU* 4.0 10.1 - - + -
430B TYR 2.8 13.7 + - - +
431B LEU* 3.5 23.9 - - + -
432B VAL 3.5 14.2 + - - -
452B ILE* 1.3 74.1 - - - +
454B PRO* 1.3 76.3 - - + +
455B LEU* 3.6 7.4 + - + +
475B GLU* 5.3 1.8 - - - +
478B THR* 3.8 20.2 - - - +
479B MET* 4.0 22.2 - - + +
482B THR* 5.1 3.8 - - - +
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Residues in contact with PRO 454 (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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415B LYS 3.6 18.6 - - - +
417B THR* 5.6 1.6 - - - +
432B VAL* 3.5 9.6 - - + +
434B GLY 3.8 19.7 - - - +
435B ASP* 4.0 22.7 - - - +
438B GLY* 4.0 20.2 - - - -
452B ILE* 4.0 7.2 - - + -
453B LEU* 1.3 97.0 - - + +
455B LEU* 1.3 63.0 + - - +
456B ARG* 3.8 7.9 + - + +
475B GLU* 4.0 5.2 - - - +
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Residues in contact with LEU 455 (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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431B LEU* 3.8 25.1 - - + +
432B VAL 2.8 14.9 + - - +
433B GLU* 4.2 4.1 - - - +
434B GLY* 3.2 18.9 + - - -
453B LEU* 4.1 13.5 - - + +
454B PRO* 1.3 74.7 - - - +
456B ARG* 1.3 60.2 + - - +
457B GLY 2.9 13.4 + - - +
459B VAL* 4.0 25.4 - - + -
475B GLU* 3.6 16.2 - - + +
479B MET* 4.3 24.5 - - + -
503B ILE* 5.7 0.2 - - + -
505B THR* 6.3 0.2 - - + -
514B ILE* 4.7 8.5 - - + +
518B LEU* 3.5 33.0 - - + -
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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