Contacts of the strand formed by residues 305 - 310 (chain A) in PDB entry 4DKT
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 PRO 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLN 3.6 3.7 - - - +
304A PRO* 1.3 91.3 - - + +
306A GLN* 1.3 63.3 + - - +
330A ALA* 4.4 7.9 - - + +
331A LYS 4.9 3.1 - - - +
332A CYS* 3.6 25.3 - - - -
592A LEU* 4.0 20.6 - - + -
593A GLY* 3.6 31.9 - - - +
649A VAL* 4.0 10.1 - - + -
650A ARG 3.8 6.5 - - - +
651A ARG* 4.1 8.3 - - + +
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Residues in contact with GLN 306 (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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304A PRO 4.5 0.9 - - - +
305A PRO* 1.3 79.5 - - - +
307A GLU* 1.3 61.0 + - - +
331A LYS 4.3 2.6 - - - +
332A CYS* 3.4 10.2 - - - -
333A LYS* 3.3 17.7 + - - +
650A ARG* 2.9 52.9 + - - +
651A ARG 3.2 21.1 - - - +
652A LYS* 3.4 30.3 - - + +
653A PRO* 4.2 6.3 - - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN* 1.3 78.7 - - - +
308A VAL* 1.3 67.7 + - - +
309A TYR* 2.8 39.6 + - + -
333A LYS* 3.6 29.3 - - + +
335A THR* 3.1 21.8 - - - +
389A PHE* 4.1 7.4 - - - -
649A VAL* 3.7 2.1 - - - +
650A ARG* 3.0 71.3 + - + +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 1.3 79.9 - - - +
309A TYR* 1.3 75.5 + - - +
310A ALA* 5.8 0.7 - - + -
323A VAL* 4.5 17.5 - - + -
327A ALA* 4.3 3.4 - - + -
332A CYS* 3.7 21.8 - - + -
333A LYS 2.8 14.9 + - - +
334A LEU* 3.3 13.7 - - + -
335A THR* 3.1 30.5 + - - +
590A LEU* 4.9 3.4 - - + -
592A LEU* 3.8 30.5 - - + -
647A THR* 4.1 13.2 - - - +
648A ASN 3.7 9.6 - - - +
649A VAL* 4.5 5.8 - - + -
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Residues in contact with TYR 309 (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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307A GLU* 2.8 45.9 + - + -
308A VAL* 1.3 77.7 - - - +
310A ALA* 1.3 59.8 + - - +
335A THR* 3.8 16.2 - - + +
348A MET* 3.2 23.8 - - + -
352A MET* 3.5 12.3 - - + -
354A ILE* 5.1 9.4 - - + -
379A PHE* 3.1 30.1 - + - -
383A ARG 5.1 0.3 - - - -
384A VAL* 3.2 32.3 - - + +
389A PHE* 4.7 5.8 - + - -
647A THR* 2.8 25.8 + - - -
648A ASN* 2.7 41.9 + - + +
650A ARG* 5.2 3.6 - - + -
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Residues in contact with ALA 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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308A VAL* 5.8 0.2 - - + -
309A TYR* 1.3 77.0 - - - +
311A CYS* 1.3 62.2 + - - +
319A PHE* 5.2 11.9 - - + -
320A LEU* 5.9 3.8 - - + -
323A VAL* 5.4 11.7 - - + -
335A THR 3.1 6.3 + - - +
336A ILE* 3.0 41.2 - - + +
337A CYS 3.2 2.1 + - - -
348A MET* 4.2 8.8 - - - +
379A PHE* 6.2 0.2 - - - -
636A TYR* 6.1 0.4 - - - +
646A GLY 3.9 15.5 - - - +
647A THR* 4.4 5.8 - - - +
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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