Contacts of the strand formed by residues 435 - 441 (chain B) in PDB entry 4B92
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 VAL 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B SER* 4.3 3.6 - - - +
405B TRP* 3.5 6.8 - - - -
406B ASP* 2.8 34.0 + - + +
409B ALA* 3.5 21.8 - - + -
411B LYS* 3.8 37.2 - - + +
432B CYS* 5.0 2.2 - - + +
434B GLY* 1.3 82.5 - - - +
436B PRO* 1.3 85.7 - - + +
437B LEU* 4.4 10.5 - - + +
447B TYR* 5.9 1.1 - - - +
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Residues in contact with PRO 436 (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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91B VAL 3.3 26.5 - - - +
92B GLY* 3.9 3.6 - - - +
93B GLY* 3.8 16.6 - - - +
356B SER* 4.3 6.1 - - - +
403B VAL* 3.7 23.3 - - + -
404B VAL 3.7 6.1 - - - +
405B TRP* 3.4 19.5 - - + -
435B VAL* 1.3 97.9 - - + +
437B LEU* 1.3 61.5 + - - +
438B VAL 4.6 0.9 - - - +
439B THR* 4.2 8.3 - - - +
447B TYR* 3.7 14.0 + - + -
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Residues in contact with LEU 437 (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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52B ASP 5.6 4.3 - - - +
56B LYS* 3.8 35.7 - - + +
404B VAL* 2.9 16.7 + - + +
406B ASP* 4.0 22.7 - - + +
435B VAL* 3.4 10.1 + - + -
436B PRO* 1.3 76.4 - - - +
438B VAL* 1.3 70.2 + - + +
447B TYR* 3.7 7.4 - - - +
448B GLU* 3.6 17.2 - - - -
449B ASN* 3.9 10.3 + - - +
450B GLY 4.8 0.9 + - - -
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Residues in contact with VAL 438 (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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51B ILE* 4.0 29.6 - - + -
403B VAL* 3.5 8.0 - - - +
404B VAL* 2.9 40.7 + - + -
436B PRO* 5.0 0.4 - - - -
437B LEU* 1.3 91.9 - - + +
439B THR* 1.3 65.4 + - - +
440B ILE* 4.0 23.1 - - + -
445B VAL* 3.9 20.4 - - + -
447B TYR* 3.2 9.2 - - - +
448B GLU* 4.1 19.3 - - + +
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Residues in contact with THR 439 (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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90B LEU* 2.7 54.6 + - + +
93B GLY* 4.1 9.0 - - - -
94B THR 4.9 0.4 - - - +
95B THR* 3.9 17.9 - - + -
402B VAL 4.0 2.0 - - - -
403B VAL* 4.1 6.4 - - + +
436B PRO* 4.2 4.3 - - - +
438B VAL* 1.3 74.6 + - - +
440B ILE* 1.3 64.2 + - - +
445B VAL* 3.8 0.5 - - - -
446B VAL* 2.9 30.6 + - + +
447B TYR* 2.9 28.1 + - - -
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Residues in contact with ILE 440 (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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10B ILE* 4.1 6.7 - - + -
12B ILE* 3.7 31.0 - - + -
30B ILE* 4.3 12.8 - - + -
51B ILE* 3.7 19.7 - - + -
95B THR* 3.7 5.5 - - - +
400B ALA 3.4 16.4 - - - +
401B ASP* 3.4 2.9 - - - -
402B VAL* 2.8 46.5 + - + +
404B VAL* 5.2 2.0 - - + -
438B VAL* 4.0 8.1 - - + -
439B THR* 1.3 72.6 - - - +
441B SER* 1.3 60.7 + - - +
443B GLY* 3.7 7.4 - - - -
444B ARG 3.1 22.7 - - - +
445B VAL* 3.7 22.2 - - + -
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Residues in contact with SER 441 (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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90B LEU* 4.0 22.7 - - - -
95B THR* 4.4 6.1 + - - -
125B CYS 4.0 4.3 + - - -
126B CYS* 3.8 23.0 - - - +
127B ASP 4.5 0.5 + - - -
400B ALA 3.9 0.4 - - - -
401B ASP* 3.9 6.7 + - - +
439B THR 4.0 1.4 + - - -
440B ILE* 1.3 73.4 - - - +
442B ARG* 1.3 80.1 + - - +
443B GLY 3.1 1.6 - - - -
444B ARG* 2.9 23.1 + - - +
446B VAL* 4.2 14.5 - - - +
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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