Contacts of the strand formed by residues 309 - 314 (chain A) 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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A PRO* 5.2 1.3 - - + -
254A LYS* 3.8 37.5 - - + +
255A LEU* 4.1 27.4 - - + +
283A ILE* 3.7 30.3 - - + -
284A VAL 3.6 3.4 - - - +
285A ASP* 3.7 8.1 - - - +
307A ALA 4.6 0.4 - - - +
308A PRO* 1.3 78.1 - - - +
310A CYS* 1.3 62.0 + - - +
311A LEU 4.0 0.3 + - - -
324A ALA 3.8 0.9 - - - +
325A ILE* 3.5 4.2 - - - +
326A GLN* 2.7 56.2 + - - +
328A ASN 4.3 1.3 - - - +
329A GLN* 3.6 20.2 - - - +
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Residues in contact with CYS 310 (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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232A PHE* 3.9 26.7 - - - -
236A PHE* 4.5 2.7 - - + -
283A ILE* 3.3 9.2 - - - +
284A VAL* 2.8 49.4 + - + +
286A PHE* 5.5 0.9 - - + -
308A PRO 4.1 0.4 - - - -
309A ILE* 1.3 72.5 - - - +
311A LEU* 1.3 65.1 + - - +
312A LEU* 3.6 23.7 - - - +
322A PRO* 4.3 2.7 - - - -
324A ALA 3.7 2.7 - - - -
325A ILE* 4.1 18.2 - - + -
354A VAL* 4.5 15.3 - - + -
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Residues in contact with LEU 311 (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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248A CYS* 4.9 2.5 - - - -
251A LEU* 4.0 18.6 - - + -
252A PRO* 5.4 0.2 - - + -
255A LEU* 4.2 16.4 - - + -
257A VAL* 3.8 28.7 - - + -
272A LEU* 4.4 5.8 - - + -
281A ILE* 3.5 30.1 - - + -
282A PHE 3.5 6.5 - - - +
283A ILE* 4.4 14.6 - - + -
309A ILE 4.0 1.0 + - - -
310A CYS* 1.3 72.7 - - - +
312A LEU* 1.3 59.7 - - - +
322A PRO* 3.6 2.9 - - - +
323A ILE* 2.9 45.1 + - + +
324A ALA* 2.9 25.8 + - + +
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Residues in contact with LEU 312 (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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233A GLY* 4.3 5.8 - - - -
236A PHE* 3.7 28.0 - - + -
245A ILE* 4.4 7.9 - - + -
281A ILE* 3.5 10.7 - - - +
282A PHE* 2.7 43.6 + - + +
283A ILE 4.3 0.4 - - - +
284A VAL* 4.0 21.1 - - + -
310A CYS* 3.6 26.9 - - - +
311A LEU* 1.3 78.3 - - - +
313A TYR* 1.3 62.9 + - - +
320A ILE* 3.6 22.4 - - + -
321A VAL 3.2 6.3 - - - +
322A PRO* 3.8 21.3 - - + -
323A ILE* 4.6 1.3 - - - -
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Residues in contact with TYR 313 (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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265A SER 3.4 27.1 - - - -
266A LEU* 3.8 14.4 - - + -
267A GLU* 3.1 22.1 + - + +
268A ARG* 2.9 28.4 + - - +
275A GLU* 2.7 39.0 + - - -
280A ASN* 3.5 14.4 - - + -
281A ILE* 3.7 11.7 - - + -
312A LEU* 1.3 77.4 - - - +
314A LYS* 1.3 58.6 + - - +
315A ASN* 3.4 20.5 + - + -
319A LYS 3.2 4.2 - - - +
320A ILE* 4.1 3.6 - - - -
321A VAL* 2.7 40.8 + - + +
323A ILE* 3.5 25.4 - - + -
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Residues in contact with LYS 314 (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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268A ARG* 2.8 34.0 + - - +
279A GLY 4.8 7.4 - - - -
280A ASN* 3.0 38.4 + - - +
282A PHE* 4.0 16.7 - - + -
313A TYR* 1.3 71.8 - - - +
315A ASN* 1.3 59.8 + - - +
318A ASN* 3.4 42.8 + - + +
319A LYS 3.3 4.0 - - - -
320A ILE* 4.1 12.0 - - + +
464A ASP* 3.0 37.8 + - - +
465A ILE* 4.8 8.3 - - + -
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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