Contacts of the strand formed by residues 408 - 414 (chain B) in PDB entry 3S95
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 ARG 408 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B LEU* 5.8 3.8 - - + -
373B PHE* 3.4 49.8 - - + +
378B GLN* 6.0 2.4 - - - +
404B TYR* 3.3 6.6 - - - -
405B LYS* 2.9 36.9 + - + +
406B ASP* 3.6 19.8 + - + +
407B LYS* 1.3 92.5 + - - +
409B LEU* 1.3 66.2 + - - +
410B ASN* 3.6 9.3 + - - +
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Residues in contact with LEU 409 (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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370B LEU* 5.4 2.6 + - - +
381B PHE* 3.2 20.4 - - + -
382B LEU* 3.9 29.6 - - + -
385B VAL* 4.1 27.1 - - + -
389B ARG* 5.6 2.5 - - - +
402B VAL* 3.7 21.1 - - + -
403B LEU 3.6 3.4 - - - +
404B TYR* 3.6 39.1 - - + +
407B LYS 4.1 1.0 + - - -
408B ARG* 1.3 72.7 - - - +
410B ASN* 1.3 84.2 + - - +
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Residues in contact with ASN 410 (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 MET* 3.3 26.2 - - + +
368B LYS 3.5 8.3 - - - +
369B GLU* 3.1 46.0 + - - +
370B LEU 4.5 1.6 + - - -
381B PHE* 4.2 1.1 - - - -
402B VAL* 3.5 0.7 - - - -
403B LEU* 2.8 48.2 + - + +
405B LYS* 4.0 9.5 - - - +
408B ARG* 3.6 12.1 + - - +
409B LEU* 1.3 92.8 - - - +
411B PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 411 (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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1B STU 4.6 2.7 - + - -
366B VAL 3.8 0.2 - - - +
367B MET* 3.3 4.5 - - - +
368B LYS* 2.9 58.0 + - + -
381B PHE* 3.6 17.9 - + - -
384B GLU* 3.5 36.6 - - + -
385B VAL* 3.3 30.1 - - + -
388B MET* 4.3 11.4 - - + -
399B PHE* 3.7 22.0 - + + -
401B GLY 3.5 11.4 - - - +
402B VAL* 4.3 2.9 - - + +
410B ASN* 1.3 75.8 - - - +
412B ILE* 1.3 64.7 + - - +
413B THR* 3.5 30.1 - - + -
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Residues in contact with ILE 412 (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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334B PHE* 3.8 23.3 - - + -
339B LEU* 4.0 20.2 - - + -
356B VAL* 4.4 1.3 - - + -
365B MET* 3.7 38.4 - - + -
366B VAL 3.1 6.3 - - - +
367B MET* 3.5 38.4 - - + +
399B PHE* 3.8 4.5 - - - -
400B ILE* 2.8 28.2 + - + -
401B GLY 2.9 22.7 + - - +
402B VAL 4.7 5.2 - - - +
403B LEU* 4.6 4.0 - - + -
411B PHE* 1.3 74.7 - - - +
413B THR* 1.3 69.5 + - - +
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Residues in contact with THR 413 (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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1B STU 3.2 20.3 + - + -
365B MET* 3.4 8.5 - - - +
366B VAL* 2.7 35.7 + - + +
368B LYS* 5.8 1.1 - - + -
388B MET* 3.5 27.8 - - + -
397B LEU* 3.9 12.3 - - + -
398B LYS 3.3 11.9 - - - -
400B ILE* 3.5 8.1 - - - +
411B PHE* 3.5 21.1 - - + -
412B ILE* 1.3 77.9 - - - +
414B GLU* 1.3 72.2 + - - +
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Residues in contact with GLU 414 (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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1B STU 2.8 29.6 + - - -
364B VAL 5.4 0.2 - - - -
365B MET* 4.9 0.7 - - - +
366B VAL* 3.9 1.0 - - - +
396B VAL 4.0 2.9 - - - +
397B LEU* 3.6 16.0 - - + -
398B LYS* 2.8 47.0 + - + +
400B ILE* 3.5 16.4 - - + +
413B THR* 1.3 80.3 + - - +
415B TYR* 1.3 53.9 + - - +
416B ILE* 3.4 23.8 - - + +
469B ARG* 2.9 28.5 + - - -
475B VAL* 4.4 0.5 - - - +
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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