Contacts of the strand formed by residues 426 - 434 (chain B) in PDB entry 3DL2
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 PHE 426 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B GLU* 3.0 43.7 + - - +
300B THR* 3.5 25.4 - - + -
301B TYR* 3.7 25.1 - + + -
304B TRP* 3.6 50.3 - + + -
311B ALA* 4.7 4.7 - - + -
314B VAL 3.6 20.0 - - - -
412B SER* 4.0 5.2 - - - -
413B ALA* 3.2 15.9 - - - +
414B LEU* 3.3 40.8 - - + -
425B VAL* 1.3 77.6 - - - +
427B LEU* 1.3 63.3 + - - +
462B ILE* 4.4 1.7 - - - +
466B GLN* 5.0 1.8 - - - +
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 4.5 2.2 - - - -
347B GLY* 3.7 26.0 - - - +
348B GLU* 3.7 5.4 - - - +
412B SER* 3.9 2.7 - - - -
413B ALA* 2.9 28.6 + - - +
415B ALA* 4.0 13.0 - - + -
421B ILE* 3.6 31.0 - - + -
425B VAL* 3.9 7.2 + - + -
426B PHE* 1.3 73.3 - - - +
428B SER* 1.3 65.8 + - - +
429B LEU* 3.4 6.6 + - + +
455B LEU* 3.7 29.8 - - + +
458B SER* 3.9 10.3 - - - -
459B ALA* 4.3 6.3 - - + +
462B ILE* 3.8 27.8 - - + -
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 5.4 0.2 + - - -
318B GLY* 4.1 5.8 - - - -
319B CYS* 2.9 36.9 + - - -
346B ILE* 3.2 9.7 - - - +
347B GLY 2.8 44.7 + - - -
410B SER* 2.7 34.1 + - - -
411B VAL 3.2 7.9 + - - -
412B SER* 4.0 2.0 + - - +
427B LEU* 1.3 69.4 - - - +
429B LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 5.2 1.8 - - + -
409B HIS 3.3 0.2 - - - +
410B SER* 3.9 4.7 - - - -
411B VAL 2.9 24.0 + - - +
413B ALA* 4.6 4.5 - - + +
414B LEU 4.5 3.6 - - - +
415B ALA* 4.3 17.5 - - + -
418B TYR* 4.0 31.4 - - + -
419B TYR* 3.8 32.1 - - + +
427B LEU* 3.9 11.0 - - + +
428B SER* 1.3 81.9 - - - +
430B PRO* 1.4 78.3 - - + +
431B CYS* 3.1 14.1 + - - -
441B VAL* 4.2 21.3 - - + -
455B LEU* 4.7 8.7 - - + -
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Residues in contact with PRO 430 (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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344B TRP* 4.1 24.5 - - + -
346B ILE* 3.9 15.7 - - + -
408B VAL* 3.8 13.9 - - + -
409B HIS 3.5 7.0 - - - +
410B SER* 4.0 4.2 - - - -
419B TYR* 5.8 1.8 - - - +
429B LEU* 1.4 87.1 - - + +
431B CYS* 1.3 58.4 + - - +
441B VAL* 3.7 5.0 - - + -
442B ILE* 3.0 43.6 + - + +
444B THR* 3.7 28.9 - - + +
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Residues in contact with CYS 431 (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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407B LYS 3.5 0.5 - - - +
408B VAL* 3.2 4.2 - - - +
409B HIS* 2.7 42.8 + - - +
411B VAL* 4.0 13.9 - - + -
413B ALA* 4.0 20.2 - - - -
429B LEU* 3.1 15.9 + - - -
430B PRO* 1.3 76.6 - - - +
432B ILE* 1.3 63.7 + - - +
433B LEU* 3.6 5.2 + - + +
438B VAL* 3.9 19.7 - - + -
440B GLU 3.3 6.7 - - - +
441B VAL* 3.8 25.4 - - - -
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Residues in contact with ILE 432 (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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406B LYS* 3.5 39.3 - - + +
407B LYS 3.7 4.0 - - - -
408B VAL* 4.0 11.2 - - + -
431B CYS* 1.3 71.7 - - - +
433B LEU* 1.3 60.4 + - - +
438B VAL* 3.6 4.7 - - - -
439B SER* 2.9 44.7 + - - +
440B GLU* 2.8 44.8 + - + +
442B ILE* 3.8 20.8 - - + +
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Residues in contact with LEU 433 (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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315B ILE* 4.1 23.6 - - + -
397B MET* 4.4 11.0 - - + +
400B SER* 3.7 8.9 - - - +
401B ILE* 4.3 17.9 - - + -
406B LYS* 3.0 27.7 + - - -
407B LYS 3.1 15.0 + - - +
409B HIS* 3.6 37.7 - - + +
411B VAL* 4.2 11.4 - - + -
431B CYS* 4.2 12.8 - - + +
432B ILE* 1.3 75.6 - - - +
434B GLY* 1.3 58.1 + - - +
437B GLY* 3.4 4.9 - - - +
438B VAL* 3.9 31.2 - - + +
439B SER* 5.1 0.2 - - - -
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Residues in contact with GLY 434 (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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400B SER 3.8 10.1 - - - -
401B ILE* 3.3 20.9 - - - +
404B ASN* 3.3 14.6 - - - -
406B LYS* 4.0 8.6 - - - +
432B ILE 4.2 0.2 + - - -
433B LEU* 1.3 75.1 - - - +
435B THR* 1.3 65.5 + - - -
436B ASN 3.2 3.1 - - - -
437B GLY* 2.9 19.9 + - - +
439B SER* 5.1 0.2 + - - -
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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