Contacts of the strand formed by residues 430 - 435 (chain D) in PDB entry 5U03
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 HIS 430 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416D TRP* 3.4 62.2 + + + +
418D ASP* 4.1 2.3 + - + -
419D ALA* 4.0 12.9 + - + -
420D ASN 3.4 3.1 + - - -
428D THR* 3.3 11.6 - - - +
429D SER* 1.3 108.7 + - - +
431D PRO* 1.3 54.4 - - - +
432D VAL* 2.6 26.2 + - + +
488D TRP* 3.4 35.5 - + + +
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Residues in contact with PRO 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D ASN 4.1 1.6 - - - +
422D THR* 3.7 22.7 - - + -
428D THR* 3.5 23.3 - - + +
429D SER 3.4 10.3 - - - +
430D HIS* 1.3 84.6 - - - +
432D VAL* 1.3 59.6 + - - +
433D VAL 3.6 1.3 - - - -
434D VAL* 3.7 10.0 - - + +
485D ASN* 2.9 33.1 + - - +
488D TRP* 3.1 12.7 - - + +
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D VAL* 3.5 30.5 - - + -
407D VAL* 3.8 18.6 - - + +
410D SER* 4.0 13.5 - - - +
416D TRP* 5.5 1.1 - - + -
419D ALA* 3.7 22.7 - - + -
420D ASN 3.0 9.2 + - - +
430D HIS* 2.6 20.2 + - + +
431D PRO* 1.3 71.7 - - - +
433D VAL* 1.4 64.8 + - + +
483D GLU 3.6 1.0 - - - +
484D VAL* 3.7 7.8 - - + -
485D ASN* 2.8 31.9 + - - +
488D TRP* 4.1 16.8 - - + -
492D LEU* 5.8 1.3 - - + -
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Residues in contact with VAL 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D GLN* 3.3 49.8 - - + +
404D LEU* 6.1 0.2 - - + -
407D VAL* 3.8 25.4 - - + -
420D ASN 3.5 2.8 + - - -
421D SER* 3.4 24.9 - - - +
422D THR* 2.7 39.3 + - - +
432D VAL* 1.4 79.7 - - + +
434D VAL* 1.3 52.9 + - - +
482D PHE* 3.4 21.5 - - + -
483D GLU 3.6 6.3 - - - +
484D VAL* 5.3 0.9 - - - +
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Residues in contact with VAL 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D THR* 3.4 7.6 - - + -
431D PRO* 3.7 33.4 - - + +
433D VAL* 1.3 79.0 - - - +
435D ASP* 1.3 65.1 + - - +
436D MET* 3.2 15.2 + - + -
482D PHE* 3.2 7.0 - - - -
483D GLU 2.7 39.5 + - - +
484D VAL 4.3 1.6 - - - +
485D ASN* 3.8 26.2 - - + +
486D PRO* 5.1 1.1 - - + -
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Residues in contact with ASP 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D THR* 3.8 3.5 + - - +
434D VAL* 1.3 72.8 - - - +
436D MET* 1.4 63.4 + - - +
437D PRO* 3.2 19.1 - - - +
481D ARG* 3.2 33.0 + - - +
482D PHE* 3.3 28.9 - - + -
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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