Contacts of the helix formed by residues 389 - 402 (chain A) in PDB entry 3D8F
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 ARG 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLU* 2.9 48.2 + - - +
384A GLU* 2.9 25.5 - - - +
386A ALA* 2.9 16.6 + - + +
387A PRO 4.5 0.7 - - - +
388A GLY* 1.3 75.8 - - - +
390A SER* 1.3 59.6 + - - +
392A VAL* 4.2 11.5 - - - +
393A ALA* 3.3 21.2 + - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU 3.3 9.2 - - - -
385A LEU* 3.8 20.2 - - - -
386A ALA 3.2 12.7 + - - -
387A PRO* 4.1 3.4 - - - -
388A GLY 4.1 7.0 - - - -
389A ARG 1.3 77.9 - - - +
391A SER* 1.3 64.4 + - - +
392A VAL 3.1 1.1 - - - -
393A ALA* 2.6 24.9 + - - +
394A VAL* 2.9 16.2 + - - +
452A VAL* 4.0 28.6 - - - +
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLY* 4.6 7.7 - - - +
389A ARG 4.6 0.6 - - - +
390A SER* 1.3 81.9 + - - +
392A VAL* 1.3 66.9 + - - +
394A VAL* 3.4 8.8 + - - +
395A ASN* 3.4 17.7 + - - +
457A ARG* 4.7 15.3 - - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLY* 4.9 7.6 - - - +
389A ARG* 4.2 21.3 - - - +
390A SER 3.1 0.4 - - - -
391A SER* 1.3 77.3 + - - +
393A ALA* 1.3 66.4 + - - +
395A ASN* 2.9 19.1 + - - +
396A ASN* 2.9 21.9 - - - +
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Residues in contact with ALA 393 (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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380A MET* 3.6 25.1 - - + -
384A GLU* 3.8 18.4 - - + +
389A ARG* 3.3 17.4 + - - +
390A SER 2.6 9.9 + - - +
392A VAL* 1.3 75.2 - - - +
394A VAL* 1.3 65.6 + - - +
395A ASN 2.8 1.6 + - - -
396A ASN* 2.9 22.1 + - - +
397A CYS* 3.2 10.2 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A MET* 4.3 6.2 - - + +
385A LEU* 5.5 1.1 - - + -
390A SER* 2.9 19.5 + - - +
391A SER* 3.9 9.0 - - - +
393A ALA* 1.3 70.2 - - - +
395A ASN* 1.3 64.2 + - - +
397A CYS* 3.0 19.9 + - - +
398A ILE* 3.0 16.9 + - + +
452A VAL* 4.5 15.0 - - + -
453A TRP 4.7 17.3 - - - +
454A GLY* 4.9 5.4 - - - -
466A ALA* 3.8 28.0 - - + -
468A VAL* 4.1 22.9 - - + -
479A CYS* 4.3 2.9 - - - -
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Residues in contact with ASN 395 (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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391A SER 3.4 7.6 + - - +
392A VAL* 2.9 12.7 + - - +
393A ALA 2.8 0.4 + - - -
394A VAL* 1.3 80.9 - - - +
396A ASN* 1.3 53.3 + - - +
398A ILE* 3.0 9.7 + - - +
399A ARG* 2.8 48.1 + - - +
455A VAL 3.6 7.8 - - - +
456A GLY* 3.9 6.0 - - - -
457A ARG* 3.1 42.7 + - - +
458A ASP* 3.2 25.5 + - - -
461A ARG* 5.6 1.6 - - - +
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Residues in contact with ASN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A VAL* 2.9 34.4 - - - +
393A ALA* 2.9 11.4 + - - +
395A ASN* 1.3 76.7 - - - +
397A CYS* 1.3 53.5 + - - +
399A ARG* 3.1 36.4 + - - +
400A GLN* 2.8 40.7 + - + +
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Residues in contact with CYS 397 (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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378A VAL* 3.8 27.4 - - + -
380A MET* 4.1 18.4 - - - -
393A ALA 3.2 9.3 + - - -
394A VAL 3.0 14.8 + - - +
396A ASN* 1.3 78.9 - - - +
398A ILE* 1.3 57.4 + - - +
400A GLN* 3.6 9.7 + - - +
401A LEU* 3.6 14.4 - - - +
479A CYS* 3.6 38.4 - - + -
481A VAL* 3.5 14.1 - - + +
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Residues in contact with ILE 398 (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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394A VAL* 3.0 20.3 + - + +
395A ASN* 3.0 9.8 + - - +
397A CYS* 1.3 75.5 - - - +
399A ARG* 1.3 66.2 + - - +
400A GLN 3.1 0.2 - - - -
402A SER* 3.2 27.7 + - - +
455A VAL* 4.1 6.3 - - - +
456A GLY* 3.9 27.4 - - - +
461A ARG* 4.2 11.1 + - - -
464A ASP* 3.4 41.5 - - + +
465A PHE 4.7 0.4 - - - -
466A ALA* 3.6 31.2 - - + +
481A VAL* 4.1 10.8 - - + -
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN* 2.8 39.7 + - - +
396A ASN* 3.2 38.1 - - - +
398A ILE* 1.3 79.0 - - - +
400A GLN* 1.3 61.0 + - + +
401A LEU 3.6 0.2 + - - -
402A SER 3.9 1.9 - - - +
458A ASP* 3.7 9.9 + - - +
461A ARG* 3.4 39.3 + - - +
487B PRO* 4.5 0.9 - - - +
490B ASN* 3.4 11.3 + - - +
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 4.8 6.0 - - + +
396A ASN* 2.8 19.2 + - + +
397A CYS* 3.9 8.3 - - - +
398A ILE 3.1 0.8 - - - -
399A ARG* 1.3 79.1 - - + +
401A LEU* 1.3 64.2 + - + +
368B LYS* 3.2 40.6 + - - +
370B PHE* 3.6 9.4 - - - -
486B ALA* 3.5 9.7 - - - +
490B ASN* 2.8 62.8 + - - +
493B THR* 5.2 8.1 - - - +
494B SER* 3.6 5.0 + - - -
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.9 18.8 - - + +
376A GLY* 3.4 38.4 - - - +
377A TRP* 3.5 6.5 - - - +
378A VAL* 3.6 30.3 - - + -
397A CYS 3.6 8.5 - - - +
398A ILE 3.4 1.4 + - - -
400A GLN* 1.3 78.2 - - + +
402A SER* 1.3 60.0 + - - +
481A VAL* 3.8 21.3 - - + -
369B CYS 4.2 6.7 - - - +
370B PHE* 3.4 35.7 - - + -
485B GLU* 3.5 10.0 - - - +
486B ALA* 3.4 19.1 - - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.4 14.5 - - - +
398A ILE* 3.2 16.2 + - - -
399A ARG 3.9 0.2 - - - +
400A GLN 3.7 0.4 - - - -
401A LEU* 1.3 81.9 - - - +
403A TYR* 1.3 54.3 + - - +
461A ARG* 2.5 35.3 + - - -
464A ASP* 2.7 29.8 + - - -
481A VAL* 4.5 1.8 - - - -
483A ARG* 2.7 25.2 + - - +
485B GLU 3.9 1.3 - - - -
486B ALA* 4.2 0.2 - - - +
487B PRO* 3.8 5.7 - - - +
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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