Contacts of the strand formed by residues 320 - 326 (chain B) in PDB entry 3V98
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 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 4.5 3.1 - - - +
233B GLY* 3.5 26.7 - - - +
234B TYR* 4.2 1.4 + - - -
237B LEU* 4.2 30.5 - - + +
245B ILE* 4.2 17.5 - - + -
282B PHE* 4.0 30.7 - - + -
312B LEU* 3.5 33.0 - - + -
313B TYR 3.3 5.4 - - - +
314B LYS* 4.2 19.1 - - + -
318B ASN 5.1 1.8 - - - +
319B LYS* 1.3 75.9 - - - +
321B VAL* 1.3 67.5 + - - +
459B MET* 4.8 0.4 - - + -
465B ILE* 4.6 9.6 - - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 4.3 7.0 - - + +
230B LEU* 3.6 39.9 - - + +
265B SER* 6.2 0.7 - - - -
312B LEU* 3.2 5.9 - - - -
313B TYR* 2.7 52.1 + - + +
315B ASN* 4.4 15.5 - - + +
319B LYS 4.4 1.8 - - - +
320B ILE* 1.3 80.7 - - - +
322B PRO* 1.3 74.5 - - + +
323B ILE* 3.7 5.4 + - + +
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Residues in contact with PRO 322 (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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229B ASP* 3.5 32.0 - - + +
232B PHE* 3.4 38.6 - - + -
233B GLY 4.4 0.9 - - - +
310B CYS* 4.2 7.4 - - - -
311B LEU 3.6 7.2 - - - +
312B LEU* 3.7 8.2 - - + -
321B VAL* 1.3 91.9 - - + +
323B ILE* 1.3 62.6 + - - +
324B ALA 3.8 0.2 - - - -
325B ILE* 4.8 0.7 - - + -
340B PRO* 4.2 5.9 - - - +
347B TRP* 3.7 31.4 - - + -
351B LYS* 4.5 1.1 - - + -
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Residues in contact with ILE 323 (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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262B VAL* 3.7 28.2 - - + +
265B SER* 3.5 28.2 + - - +
266B LEU* 4.6 4.3 - - + -
272B LEU* 4.5 1.6 - - + -
281B ILE* 4.2 13.2 - - + -
311B LEU* 2.9 42.5 + - + +
312B LEU 4.5 0.4 - - - +
313B TYR* 3.5 34.3 - - + -
321B VAL* 3.9 6.3 - - + +
322B PRO* 1.3 79.3 - - - +
324B ALA* 1.3 65.1 + - - +
339B LEU* 3.4 15.9 - - - +
340B PRO* 3.4 18.6 - - - +
347B TRP* 4.3 0.2 - - - -
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Residues in contact with ALA 324 (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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255B LEU* 5.4 4.3 - - + -
257B VAL* 4.4 9.0 - - + -
262B VAL* 4.4 8.7 - - + -
309B ILE 3.9 0.7 - - - +
311B LEU* 2.9 43.7 + - + +
322B PRO 3.8 1.0 - - - -
323B ILE* 1.3 81.7 - - + +
325B ILE* 1.3 67.0 + - - +
337B ILE* 4.0 11.9 - - + -
338B PHE 3.4 7.6 - - - -
339B LEU* 3.9 13.9 - - + -
347B TRP* 4.0 2.1 - - - -
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Residues in contact with ILE 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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232B PHE* 4.4 3.1 - - + -
308B PRO* 4.7 0.4 - - + -
309B ILE 3.5 5.8 - - - +
310B CYS* 3.9 19.7 - - + -
324B ALA* 1.3 80.1 - - - +
326B GLN* 1.3 62.6 + - - +
327B LEU* 3.5 29.8 - - + -
336B PRO 3.6 1.7 - - - +
337B ILE* 3.6 3.0 - - - +
338B PHE* 2.8 40.9 + - - +
347B TRP* 3.7 29.6 - - + -
350B ALA* 4.1 7.2 - - + +
351B LYS* 3.8 27.4 - - + +
354B VAL* 3.7 24.2 - - + -
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Residues in contact with GLN 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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254B LYS 3.0 27.6 + - - +
255B LEU* 3.6 19.3 - - + +
256B PRO* 3.7 10.7 - - - +
308B PRO* 3.1 1.7 - - - +
309B ILE* 2.7 47.0 + - + +
324B ALA 4.4 0.2 - - - -
325B ILE* 1.3 73.9 - - - +
327B LEU* 1.3 58.3 + - - +
328B ASN 3.0 22.9 + - - +
329B GLN 3.3 10.1 + - - -
331B PRO* 3.8 8.1 - - - +
335B ASN* 3.4 29.9 - - - +
336B PRO 3.9 4.7 - - - +
337B ILE* 3.6 19.8 - - + +
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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