Contacts of the strand formed by residues 361 - 366 (chain D) in PDB entry 1I43
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 ALA 361 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D LEU* 3.4 16.0 - - + +
239D PHE* 3.7 35.7 - - + -
262D PHE* 4.7 2.6 - - + -
339D TYR* 3.2 21.8 - - - -
358D PHE 4.5 0.9 - - - +
359D GLY* 3.4 1.9 - - - -
360D GLY* 1.3 80.3 - - - +
362D VAL* 1.3 61.0 + - - +
389D PHE* 5.3 6.7 - - + -
423D ARG* 5.0 11.2 - - + -
424D PHE 3.5 6.5 - - - +
425D SER* 4.7 4.0 - - - +
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LEU* 4.3 0.2 - - - -
321D ALA* 3.7 23.8 - - + +
325D ALA* 4.4 7.9 - - + -
328D LEU* 4.4 6.5 - - + -
337D VAL* 4.3 12.8 - - + -
338D TYR 3.9 11.0 - - - +
339D TYR* 3.4 22.0 - - + -
361D ALA* 1.3 80.7 - - - +
363D SER* 1.3 68.9 + - - +
364D PHE* 4.0 13.4 - - + -
422D VAL 3.9 0.9 - - - +
423D ARG* 4.7 0.6 - - - +
424D PHE* 2.8 36.7 + - - +
426D PHE* 3.7 22.7 - - + -
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Residues in contact with SER 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D PRO* 2.7 31.2 + - - +
214D LEU* 4.3 3.0 - - - +
337D VAL* 3.6 1.9 - - - +
338D TYR* 2.5 51.2 + - - +
361D ALA* 6.1 0.3 - - - +
362D VAL* 1.3 72.3 - - - +
364D PHE* 1.3 59.9 + - - +
421D LEU* 4.0 16.6 - - - -
422D VAL 3.3 5.4 - - - -
423D ARG* 3.2 23.0 - - - +
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Residues in contact with PHE 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D LEU* 3.6 35.0 - - + -
334D VAL* 4.4 14.1 - - + -
336D HIS 3.1 15.3 - - - +
337D VAL* 3.7 15.3 - - + +
338D TYR* 4.1 3.1 - - - -
362D VAL* 4.0 7.2 - - + -
363D SER* 1.3 79.3 - - - +
365D GLU* 1.3 62.5 + - - +
366D VAL* 4.0 17.0 - - + -
376D PHE* 3.7 31.6 - + - -
421D LEU* 4.2 1.5 - - - +
422D VAL* 2.8 55.9 + - + +
424D PHE* 3.9 29.2 - + + -
438D ILE* 5.2 1.3 - - + -
442D LEU* 5.9 0.7 - - + -
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Residues in contact with GLU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D PHE* 4.7 3.5 - - - -
334D VAL* 3.7 4.9 - - - +
335D ARG* 2.9 36.8 + - + +
336D HIS* 2.8 27.3 + - + +
338D TYR* 3.0 36.2 + - + -
364D PHE* 1.3 77.7 - - - +
366D VAL* 1.3 62.3 + - - +
416D GLY 5.0 0.9 - - - +
418D MET* 4.2 20.6 - - - +
420D ASN* 3.6 24.9 - - + +
421D LEU* 4.4 11.1 - - + +
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Residues in contact with VAL 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D LYS 3.8 9.9 - - - +
334D VAL* 4.6 1.8 - - + +
335D ARG* 4.2 3.3 + - - +
364D PHE* 4.0 18.2 - - + -
365D GLU* 1.3 73.4 - - - +
367D ASP* 1.3 70.5 + - - +
368D GLY 2.9 9.8 + - - +
372D THR* 4.5 8.7 - - + -
373D THR* 4.0 19.3 - - + +
376D PHE* 4.0 27.1 - - + -
420D ASN* 3.1 27.1 + - - +
422D VAL* 4.5 9.9 - - + -
442D LEU* 5.2 4.9 - - + -
445D ILE* 4.0 24.5 - - + -
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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