Contacts of the strand formed by residues 399 - 408 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A TYR* 3.3 50.0 + + - +
394A ARG 3.6 12.1 - - - +
395A GLU* 3.5 44.7 - - + +
396A GLU* 2.7 33.4 + - - -
397A VAL 3.6 0.6 - - - -
398A HIS* 1.3 79.0 - - - +
400A ALA* 1.3 81.1 + - - +
401A THR* 3.7 25.1 - - + -
417A MET* 3.9 23.1 - - + -
418A GLU 3.2 15.9 - - - +
420A LYS* 4.0 6.3 - - - +
428A VAL* 4.1 14.1 - - + -
430A LYS* 4.5 1.6 - - - -
459A VAL* 5.9 0.6 - - - +
461A GLU* 4.3 0.8 + - - -
466A ASN* 3.8 31.3 - - - +
468A PHE* 4.0 9.9 - + - -
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Residues in contact with ALA 400 (chain A).
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* 4.9 2.2 - - - -
396A GLU* 4.6 8.3 - - + +
399A TRP* 1.3 87.6 - - - +
401A THR* 1.3 66.1 + - - +
402A HIS* 4.8 1.5 - - - -
417A MET* 3.1 2.4 - - - +
418A GLU* 2.9 35.8 + - + +
420A LYS* 3.8 22.2 - - + +
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Residues in contact with THR 401 (chain A).
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* 3.4 24.5 + - - +
399A TRP* 3.7 16.4 - - + -
400A ALA* 1.3 80.3 - - - +
402A HIS* 1.3 74.8 + - - +
415A HIS* 4.2 24.7 - - + +
416A ARG 3.2 9.0 - - - -
417A MET* 4.1 0.4 - - - +
428A VAL* 4.3 5.8 - - + -
430A LYS* 5.6 3.6 - - - -
404B LEU* 4.1 13.3 - - - +
405B ARG* 5.2 12.3 + - - +
415B HIS* 5.8 1.6 + - - -
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Residues in contact with HIS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ALA 4.8 1.6 - - - -
401A THR* 1.3 86.8 + - - +
403A GLN* 1.3 71.6 + - + +
404A LEU* 3.3 8.4 + - + +
415A HIS* 4.3 5.0 - - - -
416A ARG* 2.8 51.0 + - + +
417A MET 4.0 1.6 - - - -
418A GLU* 3.3 36.8 - - + +
425A GLN* 2.7 29.4 + - - -
404B LEU* 4.5 2.7 - - - -
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Residues in contact with GLN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A HIS* 1.3 76.2 - - - +
404A LEU* 1.3 63.5 - - + +
405A ARG 3.8 1.4 + - - -
415A HIS* 4.6 5.0 + - - -
401B THR* 5.0 5.2 + - - -
402B HIS* 5.5 0.5 - - - -
403B GLN* 3.5 54.7 + - - +
404B LEU* 3.9 19.6 - - + +
415B HIS* 5.4 4.9 + - - -
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A HIS* 3.3 7.5 + - + +
403A GLN* 1.3 82.1 - - + +
405A ARG* 1.3 72.8 + - - +
406A LEU* 3.4 5.5 + - + +
415A HIS* 4.1 4.7 - - - -
416A ARG* 3.8 39.0 + - - +
401B THR* 5.7 3.4 - - - -
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Residues in contact with ARG 405 (chain A).
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 3.8 2.2 + - - -
404A LEU* 1.3 78.9 - - - +
406A LEU* 1.3 62.2 + - - +
407A GLY* 3.3 28.4 + - - +
408A ARG* 3.4 32.9 - - - +
413A GLU* 2.5 45.5 + - - -
414A VAL 3.6 5.2 - - - +
415A HIS* 3.7 19.2 - - + +
395B GLU* 3.3 34.7 + - - +
396B GLU* 3.6 47.8 + - - +
401B THR* 5.2 9.4 + - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU* 3.4 6.5 + - + -
405A ARG* 1.3 73.9 - - - +
407A GLY* 1.3 58.8 + - - +
414A VAL* 2.9 21.2 + - + +
415A HIS* 4.0 6.5 - - - +
416A ARG* 3.7 43.3 - - + +
427A ALA* 4.0 11.9 - - + -
471A LEU* 3.4 26.0 - - + -
472A LEU 5.0 0.9 - - - +
479A GLN* 4.6 6.9 + - - -
701A T28 3.4 57.4 - - + +
396B GLU* 5.7 1.4 - - - +
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ARG* 3.3 20.1 - - - +
406A LEU* 1.3 82.6 - - - +
408A ARG* 1.3 61.5 + - - -
413A GLU* 3.7 0.2 - - - -
414A VAL* 2.9 27.1 + - - +
701A T28 3.8 17.7 - - - -
396B GLU* 6.0 0.7 - - - -
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Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ARG* 3.4 30.1 - - - +
407A GLY* 1.3 75.0 - - - +
409A GLY* 1.3 71.2 + - - +
412A GLY 4.1 3.6 - - - +
413A GLU* 4.2 12.3 - - + +
701A T28 3.8 12.6 + - - -
375B GLU* 2.7 40.2 + - - -
395B GLU* 3.9 3.4 + - - +
430B LYS* 3.1 28.3 - - - +
461B GLU* 3.7 27.4 + - - +
464B TRP* 3.6 29.7 - - + +
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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