Contacts of the strand formed by residues 396 - 404 (chain B) in PDB entry 3HIG
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 THR 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308B PRO* 4.3 11.8 - - - +
310B PHE* 3.7 22.3 - - + -
312B LEU* 3.9 26.9 - - + -
394B THR 3.8 2.1 + - - -
395B ALA* 1.3 70.2 - - - +
397B PHE* 1.3 63.8 + - - +
398B LEU* 4.0 10.2 + - + +
417B CYS* 3.2 2.8 - - - -
418B LEU* 2.9 44.3 + - + +
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Residues in contact with PHE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 4.3 14.4 - - + -
386B ALA 4.9 0.2 - - - -
387B PRO* 3.6 39.5 - - + -
391B CYS* 3.8 23.8 - - + -
392B PRO 3.6 21.3 - - - -
393B GLU 4.5 5.2 - - - -
395B ALA* 3.3 23.1 + - + -
396B THR* 1.3 75.2 - - - +
398B LEU* 1.3 66.0 + - - +
399B ASP* 4.3 3.0 + - - +
414B ARG* 3.8 34.3 - - + +
416B LEU 3.5 3.4 - - - +
417B CYS* 3.8 11.7 - - + -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.6 30.7 - - + -
326B PHE* 3.6 35.2 - - + -
396B THR* 4.0 13.7 - - + +
397B PHE* 1.3 80.9 - - - +
399B ASP* 1.3 67.4 + - - +
414B ARG* 4.1 0.2 - - - -
415B ALA 2.8 25.8 + - - -
416B LEU* 2.8 38.0 + - + +
418B LEU* 5.0 10.8 - - + -
452B LEU* 5.4 2.0 - - + -
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Residues in contact with ASP 399 (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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397B PHE 4.3 2.8 + - - +
398B LEU* 1.3 82.4 - - - +
400B THR* 1.3 64.4 + - - +
401B PHE* 6.0 0.7 - - + -
411B HIS* 2.9 36.2 + - + +
412B TYR 3.4 5.8 - - - +
413B PRO* 3.5 8.9 - - - +
414B ARG* 2.8 23.4 + - - +
416B LEU* 4.5 1.9 - - - +
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Residues in contact with THR 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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35B ASP* 4.8 14.6 + - - +
36B LEU 5.7 0.3 + - - -
328B LEU* 4.2 7.6 + - + +
398B LEU 4.2 0.2 + - - -
399B ASP* 1.3 76.5 - - - +
401B PHE* 1.3 76.3 + - - +
402B HIS* 3.4 35.5 - - + +
411B HIS* 3.7 5.4 - - - -
412B TYR* 2.8 37.6 + - + -
415B ALA* 3.6 22.4 - - + -
416B LEU* 4.5 8.1 - - - -
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Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 5.7 3.3 - - - +
36B LEU 4.6 8.7 + - - +
37B SER* 5.5 1.3 - - - -
38B ASN* 3.2 57.7 - - + +
41B LEU* 3.9 23.2 - - + +
330B SER* 4.7 1.4 + - - -
399B ASP* 6.0 0.7 - - + -
400B THR* 1.3 88.3 + - - +
402B HIS* 1.3 67.8 + - - +
409B PRO* 4.5 1.6 - - + -
410B VAL 3.3 20.4 - - - -
411B HIS* 3.6 39.0 - + + -
751B VAL* 4.3 16.4 - - + -
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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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41B LEU* 4.5 3.6 - - - -
328B LEU* 4.1 15.0 - - + -
330B SER* 2.9 27.4 + - - +
379B GLY 2.8 23.4 + - - -
380B SER* 3.6 26.0 - - - -
382B THR* 3.0 23.3 + - - -
400B THR* 3.4 18.4 - - + +
401B PHE* 1.3 75.3 + - - +
403B TYR* 1.3 60.3 + - - +
404B TYR* 3.8 5.2 + - + +
410B VAL* 2.9 36.9 + - - +
412B TYR* 3.6 33.2 - + + +
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Residues in contact with TYR 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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41B LEU* 3.9 24.0 - - + +
45B HIS* 3.0 40.1 + + + -
59B SER 5.9 0.3 + - - -
68B THR* 5.4 0.7 + - - -
69B VAL* 3.1 44.2 + - + +
70B PHE 4.2 4.0 - - - -
71B LEU* 3.4 6.7 - - - +
72B ILE* 3.2 50.1 + - + +
330B SER* 4.7 2.0 + - - -
402B HIS* 1.3 71.9 - - - +
404B TYR* 1.3 62.2 + - - +
406B ALA* 3.3 27.0 + - + -
407B ASP* 4.4 0.3 + - - -
408B ASP* 3.7 14.4 - - - -
409B PRO* 3.7 26.2 - - + -
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Residues in contact with TYR 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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70B PHE* 3.5 41.6 - + - -
71B LEU* 4.3 24.5 - - + -
142B PRO* 3.9 4.3 - - - +
143B ILE 4.9 2.8 + - - -
330B SER* 4.9 4.9 - - - -
331B SER* 5.5 0.9 - - - -
375B GLY 3.8 6.9 + - - -
376B TRP* 3.3 29.8 - - - -
377B GLY* 3.3 23.7 + - - -
380B SER* 3.7 28.7 - - - -
402B HIS* 3.8 4.8 + - + +
403B TYR* 1.3 76.3 - - - +
405B ASP* 1.3 77.2 + - + +
406B ALA* 3.3 8.3 + - - +
637B ILE* 5.2 8.0 - - + +
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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