Contacts of the strand formed by residues 399 - 408 (chain B) in PDB entry 4IDT
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 TRP 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B TYR* 3.3 47.5 + + - +
394B ARG* 3.6 13.6 - - - +
395B GLU* 3.4 46.5 - - + +
396B GLU* 2.7 31.0 + - - -
397B VAL 3.6 0.6 - - - -
398B HIS* 1.3 78.6 - - - +
400B ALA* 1.3 76.5 + - - +
401B THR* 3.9 23.6 - - + -
417B MET* 3.7 17.3 - - + -
418B GLU 3.5 15.0 - - - +
419B ASP* 4.2 0.4 - - - -
420B LYS* 3.9 6.7 - - - +
428B VAL* 4.0 27.8 - - + -
430B LYS* 5.1 1.6 - - - -
459B VAL* 5.9 0.6 - - - +
461B GLU* 4.1 2.0 + - - -
466B ASN* 3.7 25.5 - - - +
468B PHE* 4.0 10.8 - + - -
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Residues in contact with ALA 400 (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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395B GLU* 4.9 2.5 - - - -
396B GLU* 4.6 11.9 - - + +
399B TRP* 1.3 89.4 - - - +
401B THR* 1.3 68.6 + - - +
417B MET* 3.1 3.1 - - - +
418B GLU* 3.0 33.8 + - + +
420B LYS* 3.4 23.3 - - - +
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Residues in contact with THR 401 (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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403A GLN 5.0 7.1 + - - -
404A LEU* 5.7 3.5 - - - +
405A ARG* 5.2 10.6 + - - +
395B GLU* 3.8 20.9 + - - +
399B TRP* 3.9 15.5 - - + -
400B ALA* 1.3 80.1 - - - +
402B HIS* 1.3 62.9 + - - +
403B GLN 5.5 0.2 + - - -
415B HIS* 3.9 30.3 - - + +
416B ARG 3.0 15.3 - - - +
428B VAL* 4.1 5.8 - - + -
430B LYS* 6.4 0.7 - - - -
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Residues in contact with HIS 402 (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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403A GLN 5.5 1.8 - - - -
401B THR* 1.3 76.7 - - - +
403B GLN* 1.3 110.6 + - + +
404B LEU 4.6 0.9 - - - +
415B HIS* 5.3 1.0 - - - -
416B ARG* 3.1 38.5 + - + +
417B MET* 3.8 19.3 - - - -
418B GLU* 3.4 40.2 - - + +
425B GLN* 3.8 26.5 + - + -
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Residues in contact with GLN 403 (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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403A GLN* 3.5 54.4 + - - +
401B THR* 5.5 0.3 + - - -
402B HIS* 1.3 100.9 + - + +
404B LEU* 1.3 68.0 + - + +
405B ARG 4.1 0.3 + - - -
415B HIS* 4.4 6.2 - - - -
416B ARG* 3.9 27.5 - - - +
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Residues in contact with LEU 404 (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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401A THR* 4.1 15.3 - - - +
402A HIS* 4.5 1.3 - - - -
403A GLN* 3.9 35.2 - - + +
402B HIS 4.6 1.6 - - - +
403B GLN* 1.3 82.8 - - + +
405B ARG* 1.3 71.1 + - - +
406B LEU* 3.2 2.9 + - - +
415B HIS* 4.2 3.5 - - - -
416B ARG* 3.7 18.7 + - - +
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Residues in contact with ARG 405 (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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395A GLU* 3.2 40.1 + - - +
396A GLU* 3.5 43.7 + - - +
401A THR* 5.2 12.1 + - - +
403B GLN 4.1 0.2 + - - -
404B LEU* 1.3 76.5 - - - +
406B LEU* 1.3 62.4 + - - +
407B GLY* 3.3 30.1 + - - +
408B ARG* 3.9 28.5 - - - +
413B GLU* 2.6 45.1 + - - -
414B VAL 3.6 4.5 - - - +
415B HIS* 3.5 25.1 + - + +
416B ARG* 5.1 1.2 + - - -
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Residues in contact with LEU 406 (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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404B LEU 3.2 3.2 + - - -
405B ARG* 1.3 76.2 - - - +
407B GLY* 1.3 59.2 + - - +
414B VAL* 2.8 28.6 + - + +
415B HIS* 3.9 17.2 - - - +
416B ARG* 3.6 44.9 - - + +
427B ALA* 4.0 4.7 - - + -
471B LEU* 3.7 24.9 - - + -
472B LEU 5.2 1.1 - - - +
479B GLN* 4.5 8.5 + - - -
701B T28 3.4 52.5 - - + +
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Residues in contact with GLY 407 (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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405B ARG* 3.3 21.5 - - - +
406B LEU* 1.3 82.7 - - - +
408B ARG* 1.3 61.5 + - - -
413B GLU* 3.7 0.3 - - - -
414B VAL* 2.9 27.8 + - - +
701B T28 3.9 16.6 - - - -
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Residues in contact with ARG 408 (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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375A GLU* 2.4 44.4 + - - -
395A GLU* 4.3 3.0 + - - +
430A LYS* 4.0 17.0 - - - +
461A GLU* 3.9 23.2 + - - +
464A TRP* 3.4 44.6 - - + +
405B ARG* 3.9 25.8 - - - +
407B GLY* 1.3 75.1 - - - +
409B GLY* 1.3 71.9 + - - +
412B GLY 3.9 5.4 - - - +
413B GLU* 4.3 7.4 - - + +
701B T28 3.8 13.5 + - - -
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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