Contacts of the strand formed by residues 411 - 418 (chain A) in PDB entry 3DDN
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 SER 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A TRP* 3.8 23.7 - - - -
354A ARG 3.3 11.0 - - - -
356A GLU* 3.3 11.8 + - - +
357A LEU* 2.9 31.8 + - - +
406A SER* 4.1 1.6 - - - -
409A HIS* 3.5 1.8 - - - +
410A ARG* 1.3 76.6 + - - +
412A VAL* 1.3 57.8 + - - +
430A THR* 2.3 40.6 - - - +
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TRP* 4.5 1.8 - - - -
352A GLN 4.0 0.3 - - - +
353A VAL* 3.9 1.0 - - - +
354A ARG* 3.0 58.4 + - + +
357A LEU* 5.1 0.3 - - - +
406A SER* 3.6 17.0 - - - +
407A PRO* 4.7 2.9 - - + -
409A HIS* 4.7 8.5 - - + -
411A SER* 1.3 76.1 - - - +
413A VAL* 1.3 68.0 + - - +
414A ASP* 3.8 17.9 - - - +
428A SER* 3.8 14.4 - - - -
429A GLY 3.6 14.4 - - - +
430A THR* 4.2 0.7 - - + -
441A VAL* 3.9 13.9 - - + -
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Residues in contact with VAL 413 (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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327A TRP* 3.8 12.1 - - + -
331A VAL* 3.8 24.0 - - + -
334A LEU* 3.5 12.5 - - + +
351A VAL* 3.8 28.5 - - + -
352A GLN 3.3 4.0 - - - +
353A VAL* 4.3 11.2 - - + -
357A LEU* 3.6 30.5 - - + -
365A LEU* 4.5 2.2 - - + -
412A VAL* 1.3 75.2 - - - +
414A ASP* 1.3 65.0 + - - +
415A VAL* 4.4 1.3 - - + -
428A SER* 3.2 2.8 - - - -
429A GLY 3.0 36.2 + - - +
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Residues in contact with ASP 414 (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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350A SER 3.5 1.6 - - - +
351A VAL* 3.5 3.6 - - - +
352A GLN* 2.8 49.9 + - - +
354A ARG* 2.4 51.6 + - - -
412A VAL* 3.8 8.9 - - - +
413A VAL* 1.3 73.7 - - - +
415A VAL* 1.3 62.7 + - - +
416A ARG 3.9 0.2 - - - -
426A THR* 4.3 12.8 - - + -
427A VAL 3.5 4.5 - - - -
428A SER* 2.5 29.4 + - - +
442A GLN* 4.5 3.3 + - - -
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Residues in contact with VAL 415 (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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331A VAL* 4.4 3.1 - - + -
334A LEU* 3.7 35.7 - - + +
335A GLY* 4.5 3.8 - - - +
338A ALA* 4.0 22.1 - - + +
349A LEU* 4.2 30.3 - - + -
350A SER 3.7 2.9 - - - +
351A VAL* 4.4 16.8 - - + -
369A ALA* 4.4 12.8 - - + -
413A VAL* 4.4 1.6 - - + -
414A ASP* 1.3 74.4 - - - +
416A ARG* 1.3 61.2 + - - +
417A ALA 3.8 0.3 + - - -
425A VAL 3.4 2.4 - - - +
426A THR* 3.4 3.6 - - - -
427A VAL 2.7 36.5 + - - +
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Residues in contact with ARG 416 (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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349A LEU* 3.2 5.0 - - - -
350A SER* 2.6 50.4 + - - +
352A GLN* 2.7 44.0 + - - +
415A VAL* 1.3 72.1 - - - +
417A ALA* 1.3 61.5 + - - +
418A VAL* 3.7 9.7 + - + +
424A VAL* 3.9 34.0 - - + +
425A VAL 3.3 4.5 - - - -
426A THR* 3.6 22.3 + - + +
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Residues in contact with ALA 417 (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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338A ALA* 3.8 17.9 - - + +
342A SER* 3.8 22.0 + - - +
346A PRO* 3.9 9.2 - - + -
348A SER 3.6 5.4 - - - -
349A LEU* 3.8 17.7 - - + -
415A VAL 3.8 1.4 + - - -
416A ARG* 1.3 71.4 - - - +
418A VAL* 1.3 59.6 + - - +
419A GLY 3.9 0.5 + - - -
423A SER 3.9 0.3 - - - +
424A VAL* 3.4 3.8 - - - -
425A VAL* 2.7 37.7 + - + +
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Residues in contact with VAL 418 (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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346A PRO* 3.3 3.5 - - - +
347A VAL* 2.8 33.3 + - + +
348A SER* 2.8 34.6 + - - +
350A SER* 4.7 9.9 - - - +
416A ARG* 4.0 17.7 - - + +
417A ALA* 1.3 74.6 - - - +
419A GLY* 1.3 70.3 + - - +
422A GLY* 5.0 6.1 - - - -
423A SER 3.5 7.4 - - - +
424A VAL* 4.2 12.8 - - + -
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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