Contacts of the strand formed by residues 418 - 425 (chain B) in PDB entry 3H3T
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 LEU 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B TRP* 4.0 2.1 - - - -
395B VAL* 5.8 1.6 - - + -
403B VAL* 3.9 21.1 - - + -
404B TYR 3.3 10.5 - - - +
405B ARG* 4.9 9.0 - - + +
416B ASP 4.3 4.3 - - - +
417B PRO* 1.3 75.3 - - - +
419B LYS* 1.3 74.6 + - - +
420B ALA* 4.4 2.5 - - + +
553B TYR* 4.3 15.7 - - + -
554B VAL* 3.4 4.3 - - - +
555B ALA* 2.9 41.6 + - + +
556B ASN* 5.2 0.7 + - - -
572B ALA* 4.7 12.3 - - + +
573B LYS* 6.1 0.2 - - - -
576B TYR* 3.4 51.1 - - + -
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Residues in contact with LYS 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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517A ARG* 5.7 3.1 - - - +
382B SER* 2.4 35.5 + - - +
383B LEU* 3.7 3.4 + - - +
384B GLN 2.7 28.5 + - - +
385B ASP* 4.8 1.5 - - - +
386B VAL* 4.1 26.5 - - + +
392B TRP* 3.7 19.6 - - + -
404B TYR* 2.6 44.2 + - + +
418B LEU* 1.3 78.3 - - - +
420B ALA* 1.3 65.5 + - - +
421B THR* 3.9 19.1 - - + -
552B THR* 3.8 13.1 + - - +
553B TYR 3.4 5.2 - - - -
554B VAL* 3.8 14.6 - - + -
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B MET* 5.2 0.2 - - + -
402B LYS 3.1 11.2 - - - +
403B VAL* 4.0 12.1 - - + -
404B TYR* 4.9 0.4 - - - -
418B LEU* 4.4 2.9 - - + +
419B LYS* 1.3 76.2 - - - +
421B THR* 1.3 68.2 + - - +
551B ILE* 4.5 0.4 - - - -
552B THR* 3.4 4.3 - - - -
553B TYR* 2.8 40.0 + - + +
580B LEU* 3.6 32.5 - - + -
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Residues in contact with THR 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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386B VAL* 5.8 0.4 - - + -
400B GLU 3.7 2.1 + - - +
401B MET* 3.4 3.8 - - - +
402B LYS* 2.9 47.4 + - - +
404B TYR* 4.4 9.7 + - + -
419B LYS* 3.9 23.6 - - + -
420B ALA* 1.3 80.7 - - - +
422B HIS* 1.3 63.9 + - - +
551B ILE 3.1 9.2 - - - -
552B THR* 4.1 10.1 - - - +
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Residues in contact with HIS 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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398B GLU 5.3 0.4 - - - -
400B GLU* 3.4 33.4 - - + +
401B MET* 3.9 32.4 - - + +
421B THR* 1.3 75.7 - - - +
423B ALA* 1.3 86.4 + - - +
424B VAL* 4.2 8.2 - - + +
550B LYS* 3.6 2.6 - - - +
551B ILE* 2.7 47.4 + - + +
580B LEU* 4.5 13.7 - - + -
581B LYS* 5.2 2.8 - - - -
584B THR* 3.9 31.0 + - + -
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Residues in contact with ALA 423 (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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400B GLU* 3.4 36.0 - - + +
422B HIS* 1.3 86.8 + - - +
424B VAL* 1.3 61.0 + - - +
425B LYS* 4.1 2.3 + - - +
548B LEU* 4.5 20.8 - - + +
549B CYS 3.3 7.4 - - - +
550B LYS* 5.1 7.4 - - + -
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Residues in contact with VAL 424 (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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422B HIS* 4.2 11.4 - - + +
423B ALA* 1.3 78.1 - - - +
425B LYS* 1.3 61.1 + - - +
426B GLY 3.7 0.3 + - - -
427B VAL* 3.8 17.7 - - + +
432B VAL* 5.7 1.6 - - + -
548B LEU* 4.1 1.3 - - - +
549B CYS* 2.8 39.3 + - + +
551B ILE* 3.7 26.9 - - + -
584B THR* 3.8 25.8 - - + +
587B VAL* 6.3 0.2 - - + -
588B GLN* 3.3 39.9 - - + +
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Residues in contact with LYS 425 (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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400B GLU* 5.6 9.0 - - - -
423B ALA 4.1 1.7 + - - +
424B VAL* 1.3 73.5 - - - +
426B GLY* 1.3 62.8 + - - +
427B VAL 3.5 0.5 + - - -
544B ARG 5.7 0.2 - - - +
547B ILE 3.9 6.7 - - - +
548B LEU* 3.7 20.0 - - + -
588B GLN* 2.8 34.2 + - - +
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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