Contacts of the helix formed by residues 485 - 501 (chain B) in PDB entry 3KF4
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 485 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A LYS* 5.4 0.7 - - - +
355B GLU* 3.5 19.3 - - - -
419B LYS* 3.5 11.9 - - - +
422B VAL* 4.7 0.7 - - - -
484B PRO* 1.3 76.9 - - - +
486B PHE* 1.3 59.7 + - - +
487B ALA* 3.5 7.3 + - - +
488B GLU* 2.9 40.7 + - - +
489B ILE* 3.0 27.1 + - - +
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Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 4.3 11.1 - - - +
351B MET* 3.3 43.1 - - + -
352B GLU* 3.5 23.3 - - - +
355B GLU* 2.8 11.4 + - - +
364B LEU* 4.2 0.2 - - + -
418B ILE* 3.6 37.5 - - + -
421B ASP* 3.5 31.6 - - + -
422B VAL* 3.6 17.7 - - + -
425B PHE* 3.7 28.3 - + + -
485B SER* 1.3 70.1 - - - +
487B ALA* 1.3 61.1 + - - +
489B ILE* 3.8 11.1 - - + +
490B HIS* 2.7 34.1 + - - +
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Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 3.1 38.6 - - + +
352B GLU* 3.3 22.1 - - + +
355B GLU* 3.0 14.7 + - - +
485B SER* 3.2 9.4 - - - +
486B PHE* 1.3 78.6 - - - +
488B GLU* 1.3 60.3 + - - +
490B HIS* 3.8 2.3 - - - +
491B GLN* 3.2 24.1 + - - +
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Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 5.3 8.1 - - + -
445A LEU* 5.1 1.4 - - - +
484B PRO* 3.9 15.3 - - + +
485B SER* 2.9 44.7 + - - +
487B ALA* 1.3 74.8 - - - +
489B ILE* 1.3 65.5 + - - +
491B GLN* 3.4 5.7 + - - +
492B ALA* 3.0 24.7 + - - +
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Residues in contact with ILE 489 (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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348B SER* 3.8 9.6 - - - -
422B VAL* 3.9 17.3 - - + -
425B PHE* 3.5 28.3 - - + -
471B LEU* 4.8 9.2 - - + -
475B CYS* 3.8 26.2 - - - -
484B PRO* 3.8 16.4 - - + -
485B SER 3.0 22.7 + - - +
486B PHE* 3.8 20.6 - - + +
488B GLU* 1.3 74.8 - - - +
490B HIS* 1.3 59.0 + - - +
492B ALA* 3.2 8.3 + - - +
493B PHE* 2.9 42.8 + - + -
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Residues in contact with HIS 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR* 3.5 20.4 + - + +
348B SER* 3.3 28.9 + - - +
349B SER* 3.6 22.1 + - - -
352B GLU* 3.4 26.4 + - - +
486B PHE 2.7 22.5 + - - +
487B ALA 3.8 1.6 - - - +
489B ILE* 1.3 75.2 - - - +
491B GLN* 1.3 64.2 + - + +
493B PHE* 3.3 1.4 + - - +
494B GLU* 2.9 62.0 + - - +
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Residues in contact with GLN 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 5.3 9.1 - - - +
401A PHE 3.2 21.1 + - - +
402A PRO* 3.5 6.3 - - - +
403A ILE* 2.8 43.6 + - - +
445A LEU* 3.6 19.4 - - + +
487B ALA 3.2 15.1 + - - +
488B GLU* 3.4 5.2 + - - +
490B HIS* 1.3 85.4 - - + +
492B ALA* 1.3 57.6 + - - +
494B GLU* 3.8 5.0 - - + +
495B THR* 2.8 40.2 + - - +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 3.6 17.6 - - + +
471B LEU* 3.8 26.2 - - + -
488B GLU 3.0 18.4 + - - +
489B ILE* 3.4 4.7 - - - +
491B GLN* 1.3 77.8 - - - +
493B PHE* 1.3 57.7 + - - +
495B THR* 3.3 3.5 + - - -
496B MET* 2.9 36.0 + - + +
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Residues in contact with PHE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.1 25.5 - - + +
344B ALA* 3.6 25.6 - - + -
345B THR* 3.5 18.9 + - - +
348B SER* 4.4 1.8 - - - +
425B PHE* 4.1 2.7 - + - -
429B LEU* 3.4 40.8 - - + -
468B VAL* 4.3 16.2 - - + -
471B LEU* 3.4 24.2 - - + -
489B ILE* 2.9 38.6 + - + +
490B HIS 4.0 2.5 - - - +
492B ALA* 1.3 72.3 - - - +
494B GLU* 1.3 56.5 + - - +
496B MET* 3.6 17.2 - - + +
497B PHE* 2.7 36.7 + - - +
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Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR* 3.8 19.6 + - + +
490B HIS* 2.9 45.5 + - - +
491B GLN* 3.8 6.9 - - + +
493B PHE* 1.3 75.5 - - - +
495B THR* 1.3 50.8 + - - +
497B PHE* 3.2 7.0 + - + +
498B GLN* 2.7 63.7 + - + +
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Residues in contact with THR 495 (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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404A LYS* 4.0 19.9 - - + +
438A SER* 5.2 2.2 - - - +
445A LEU* 3.7 22.3 - - + +
491B GLN* 2.8 29.0 + - - +
492B ALA* 3.5 5.2 - - - +
494B GLU* 1.3 77.5 - - - +
496B MET* 1.3 65.1 + - + +
498B GLN* 3.3 8.2 + - - +
499B GLU* 3.0 49.2 + - + +
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.7 14.1 - - + +
465B PRO* 6.2 0.2 - - - -
467B LYS* 4.2 22.2 - - + +
468B VAL* 3.9 22.7 - - + -
471B LEU* 3.8 21.5 - - + -
492B ALA* 2.9 29.2 + - + +
493B PHE* 3.7 28.7 - - + +
495B THR* 1.3 77.5 - - + +
497B PHE* 1.3 64.0 + - - +
499B GLU* 3.3 10.2 + - - +
500B SER* 3.0 27.4 + - - -
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Residues in contact with PHE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL* 3.7 25.1 - - + -
341B LEU* 4.2 7.8 - - + +
342B TYR* 3.5 46.4 - + + -
345B THR* 3.8 17.0 - - + +
493B PHE 2.7 21.2 + - - +
494B GLU* 3.4 9.4 - - + +
496B MET* 1.3 73.8 - - - +
498B GLN* 1.3 75.5 + - - +
500B SER* 3.5 3.4 + - - -
501B SER* 3.1 48.6 + - - -
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Residues in contact with GLN 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 5.8 8.8 - - + +
328A ARG* 3.4 36.6 + - - +
367A ARG* 5.4 10.7 - - - +
438A SER* 4.6 9.9 - - - +
494B GLU* 2.7 53.4 + - + +
495B THR* 3.6 7.6 - - - +
497B PHE* 1.3 87.1 - - - +
499B GLU* 1.3 61.1 + - - +
501B SER* 3.8 8.0 + - - -
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Residues in contact with GLU 499 (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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404A LYS* 2.9 29.6 + - - -
438A SER* 3.3 27.7 + - - +
439A PRO 3.7 9.0 - - - +
440A TYR 4.1 2.3 - - - +
441A PRO* 4.1 4.2 - - - +
442A GLY* 3.9 18.3 + - - -
495B THR* 3.0 28.1 + - + +
496B MET* 3.8 10.2 - - - +
497B PHE 3.2 0.4 - - - -
498B GLN* 1.3 79.1 - - - +
500B SER* 1.3 59.6 + - - +
501B SER 4.4 3.3 - - - -
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL* 3.6 20.9 - - - +
341B LEU* 3.0 30.0 - - - +
496B MET 3.0 12.8 + - - -
497B PHE 3.5 4.0 + - - -
499B GLU* 1.3 75.3 - - - +
501B SER* 1.3 64.1 + - - +
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Residues in contact with SER 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 4.5 18.4 + - - -
338B VAL* 3.4 19.4 - - - +
497B PHE* 3.1 32.7 + - - -
498B GLN* 4.2 13.5 - - - -
499B GLU 3.3 5.1 - - - -
500B SER* 1.3 81.6 - - - +
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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
------------------------------------------------------------
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