Contacts of the strand formed by residues 395 - 399 (chain X) in PDB entry 3Q0F
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 395 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C 5CM 4.3 5.2 - - + -
388X HIS* 3.7 1.3 - - - -
390X PRO* 3.9 9.4 - - - +
393X SER* 3.4 14.4 + - - -
394X GLY* 1.3 81.0 - - - +
396X ASP* 1.3 71.5 + - - +
397X TYR* 4.4 8.7 - - + -
407X ALA* 4.6 5.6 - - + -
409X SER 3.8 5.2 - - - +
410X ILE* 4.5 2.9 - - + -
428X TYR* 3.8 20.9 - - + +
430X GLY* 4.8 1.3 - - - -
431X GLN* 4.0 17.8 + - + +
452X GLY* 3.5 36.1 - - - +
453X ASN* 3.7 22.7 - - - +
455X ALA* 5.0 0.2 - - + -
456X LEU* 3.8 28.3 - - + -
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Residues in contact with ASP 396 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362X GLN* 3.9 4.9 + - - +
387X ILE 4.7 0.7 - - - +
388X HIS* 3.3 25.7 - - + +
389X ARG* 3.0 39.5 + - - +
390X PRO* 3.4 20.2 - - + +
395X ILE* 1.3 73.4 - - - +
397X TYR* 1.3 71.9 + - - +
407X ALA* 3.4 4.2 - - - +
408X THR* 2.7 39.7 + - - -
409X SER* 2.9 19.0 + - - +
467X ARG* 5.2 0.5 + - - -
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Residues in contact with TYR 397 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B A 4.4 5.6 + - - -
11B T 3.2 28.0 + - - -
362X GLN* 3.2 4.1 + - - -
389X ARG* 3.1 24.8 + - - -
395X ILE* 4.4 5.6 - - + -
396X ASP* 1.3 84.2 + - - +
398X MET* 1.3 66.2 + - - +
405X LEU* 3.8 32.5 - - + +
406X VAL 3.1 17.0 - - - +
408X THR* 3.9 3.1 - - - -
431X GLN* 5.5 1.3 - - - -
451X THR* 3.6 23.9 - - - +
452X GLY* 3.5 30.5 - - - -
455X ALA* 3.4 17.0 - - + -
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Residues in contact with MET 398 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362X GLN* 3.8 41.7 - - + +
364X ILE* 3.8 31.0 - - + -
389X ARG* 4.9 2.0 - - - +
397X TYR* 1.3 81.0 - - - +
399X LYS* 1.3 81.9 + - - +
400X ASP* 5.4 1.3 - - - -
405X LEU* 3.1 8.3 - - - +
406X VAL* 2.9 43.6 + - + +
408X THR* 4.1 5.4 - - + -
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Residues in contact with LYS 399 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B T 4.2 20.3 + - - -
398X MET* 1.3 99.4 - - - +
400X ASP* 1.3 64.4 + - - +
401X ASP 4.0 0.5 + - - -
403X GLY* 4.0 16.4 - - - +
404X GLU 3.2 4.5 - - - +
405X LEU* 3.9 22.7 - - + -
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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