Contacts of the strand formed by residues 324 - 334 (chain B) in PDB entry 6IWQ
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 ILE 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B PRO* 4.0 27.4 - - + +
318B ILE* 3.8 21.4 - - - +
320B LYS* 6.2 0.4 - - + -
321B ASP* 3.3 37.0 - - + +
322B ARG 3.3 2.6 - - - +
323B THR* 1.3 79.8 - - - +
325B CYS* 1.3 69.5 + - - +
326B THR* 4.2 2.2 - - - +
393B ALA 4.3 0.9 - - - +
394B ILE* 4.4 6.2 - - - +
429B LYS* 3.6 31.9 - - + +
431B LEU* 3.8 32.1 - - + -
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Residues in contact with CYS 325 (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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323B THR 3.8 0.4 + - - -
324B ILE* 1.3 76.0 - - - +
326B THR* 1.3 61.8 + - - +
387B MET* 3.8 28.0 - - - -
392B PHE* 3.9 11.7 - - - -
393B ALA 3.3 15.9 - - - -
394B ILE* 3.5 22.7 - - + -
423B ILE* 3.7 20.6 - - + -
429B LYS 2.8 11.5 + - - +
430B LEU* 3.3 8.8 - - + +
431B LEU* 2.9 26.0 + - - -
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Residues in contact with THR 326 (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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314B LEU* 3.2 48.5 + - + +
317B PRO* 3.7 19.9 - - - +
318B ILE* 3.9 6.0 - - - +
324B ILE* 4.2 3.0 + - - +
325B CYS* 1.3 74.9 - - - +
327B VAL* 1.3 64.4 + - - +
328B PRO* 4.5 0.2 - - - +
392B PHE* 3.3 4.7 - - - +
393B ALA* 2.7 44.7 + - - +
431B LEU* 3.4 4.9 + - - +
433B VAL* 3.3 24.4 - - + +
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Residues in contact with VAL 327 (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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314B LEU* 4.1 3.6 - - - -
326B THR* 1.3 76.6 - - - +
328B PRO* 1.3 77.5 - - + +
330B ILE* 4.9 8.5 - - + -
387B MET* 3.7 21.1 - - + -
388B ALA* 5.4 3.1 - - + +
391B LEU 3.4 17.5 - - - +
392B PHE* 4.1 8.1 - - + -
430B LEU* 3.5 28.3 - - + -
431B LEU 2.8 6.8 + - - +
432B PHE* 3.5 27.4 - - + -
433B VAL* 2.9 25.1 + - - +
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Residues in contact with PRO 328 (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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300B LEU* 5.8 1.3 - - + -
310B TRP* 6.1 0.4 - - + -
314B LEU* 3.5 26.2 - - + -
327B VAL* 1.3 105.0 - - + +
329B LEU* 1.3 64.5 + - - +
330B ILE* 3.4 6.4 + - - +
391B LEU* 3.7 27.4 - - + +
392B PHE* 4.4 2.5 - - - -
432B PHE* 5.6 1.2 - - - -
433B VAL 4.1 1.8 - - - +
436B SER* 3.2 21.1 - - - +
438B VAL* 3.8 32.3 - - + -
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Residues in contact with LEU 329 (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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328B PRO* 1.3 74.0 - - - +
330B ILE* 1.3 60.8 + - - +
331B ASP* 3.8 1.5 + - - +
350B GLY 4.6 6.5 - - - +
351B TYR* 3.7 28.3 - - + -
352B ALA 5.4 0.2 - - - +
382B TYR* 4.1 19.3 - - + +
432B PHE* 4.2 20.6 - - + -
433B VAL 3.7 6.7 + - - +
434B PRO* 3.7 19.7 - - + +
436B SER 3.0 10.5 + - - +
437B ARG* 3.4 44.4 - - + +
438B VAL 3.1 23.4 + - - -
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Residues in contact with ILE 330 (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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327B VAL* 4.9 4.3 - - + -
328B PRO* 3.5 16.4 - - + +
329B LEU* 1.3 72.7 - - - +
331B ASP* 1.3 65.6 + - - +
343B GLN* 3.2 31.1 - - - +
364B ARG* 5.6 0.3 + - - -
388B ALA* 4.2 25.4 - - + -
390B GLY 5.6 0.7 - - - +
391B LEU* 3.9 39.7 - - + +
438B VAL* 3.4 7.4 - - - +
440B HIS* 3.8 28.7 - - + -
442B TYR* 4.5 10.0 + - - +
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Residues in contact with ASP 331 (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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192B LEU* 3.4 21.1 - - - +
329B LEU* 4.5 5.0 - - - +
330B ILE* 1.3 80.2 + - - +
332B VAL* 1.3 62.9 + - - +
340B ILE* 3.9 14.1 - - + +
341B ILE 3.6 7.9 - - - +
342B PRO* 3.8 7.0 - - - +
343B GLN 4.3 1.8 + - - +
437B ARG* 2.9 49.2 + - - +
438B VAL 2.8 13.4 + - - +
439B GLY* 3.3 2.8 - - - +
440B HIS* 2.8 29.5 + - - +
442B TYR* 4.4 1.3 - - - -
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Residues in contact with VAL 332 (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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331B ASP* 1.3 73.0 - - - +
333B ILE* 1.3 67.0 + - - +
334B ASN* 4.8 2.5 - - - +
340B ILE* 3.3 3.0 - - - -
341B ILE* 2.7 60.1 + - + +
342B PRO 4.2 2.5 - - - +
343B GLN* 3.9 33.7 - - + +
440B HIS 3.8 1.8 - - - -
442B TYR* 3.5 39.5 - - + -
632D LEU* 6.0 0.4 - - + -
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Residues in contact with ILE 333 (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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187B ARG* 4.5 0.2 - - - +
304B CYS* 4.4 0.4 - - - -
305B GLU* 3.6 36.8 - - + +
332B VAL* 1.3 75.7 - - - +
334B ASN* 1.3 71.7 + - - +
335B GLY 3.2 3.3 + - - -
338B TYR* 3.9 20.9 - - + +
339B GLU 3.7 3.1 - - - -
340B ILE* 3.7 18.2 - - + -
439B GLY* 3.7 30.5 - - - +
440B HIS 2.8 10.7 + - - +
441B ILE* 2.3 47.4 - - + -
442B TYR* 3.4 17.3 + - - +
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Residues in contact with ASN 334 (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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332B VAL* 3.8 4.1 + - - -
333B ILE* 1.3 71.1 - - - +
335B GLY* 1.3 58.8 + - - +
336B ASN* 2.5 39.8 + - - +
337B THR* 3.1 21.7 + - - +
338B TYR* 2.9 34.3 + - - +
339B GLU* 3.1 38.8 + - - +
341B ILE* 4.5 8.9 - - + +
442B TYR* 6.2 0.2 - - - -
444B LEU* 5.2 0.5 - - - +
561D PRO* 5.0 6.3 - - - +
633D HIS* 5.7 1.6 - - - -
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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