Contacts of the helix formed by residues 452 - 470 (chain K) in PDB entry 4DVQ
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 GLY 452 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148K VAL* 4.5 6.1 - - - -
450K CYS* 3.4 8.7 - - - -
451K LEU* 1.3 76.4 - - - +
453K ARG* 1.3 53.2 + - - +
454K ARG 3.3 2.7 - - - -
455K LEU* 3.3 10.5 + - - +
456K ALA* 2.8 36.0 + - - +
601K HEM 3.6 34.7 - - - +
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Residues in contact with ARG 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LEU* 4.1 9.1 - - + +
366K ARG* 4.8 0.6 - - - +
443K PHE* 3.4 44.3 - - + -
449K GLN* 4.1 25.6 + - - +
450K CYS* 3.4 24.0 - - + +
451K LEU 3.2 2.4 - - - -
452K GLY* 1.3 76.6 - - - +
454K ARG* 1.3 88.9 + - - +
456K ALA* 3.3 1.6 + - - +
457K GLU* 2.8 54.6 + - - +
603K SO4 2.8 37.8 + - - -
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Residues in contact with ARG 454 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149K LEU* 2.9 49.9 + - + +
150K SER* 4.3 0.6 - - - +
151K PRO* 3.5 29.5 - - - +
154K VAL* 3.6 32.1 - - + +
157K PHE* 4.7 3.6 - - + -
359K THR* 5.9 1.0 - - - +
452K GLY 3.3 0.4 - - - -
453K ARG* 1.3 101.9 - - - +
455K LEU* 1.3 61.6 + - - +
457K GLU* 4.1 6.4 - - - +
458K ALA* 3.0 28.8 + - - +
603K SO4 2.5 45.6 + - - +
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Residues in contact with LEU 455 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148K VAL* 5.0 6.5 + - + +
157K PHE* 3.6 34.4 - - + -
161K VAL* 4.0 9.0 - - + -
200K SER* 4.9 5.6 - - - +
203K ALA* 3.6 22.2 - - + -
204K LEU* 4.9 10.3 - - + -
289K ILE* 4.4 17.0 - - + -
315K SER* 5.1 2.0 - - - -
452K GLY* 3.3 13.6 + - - +
454K ARG* 1.3 77.3 - - - +
456K ALA* 1.3 52.2 + - - +
458K ALA* 3.2 4.0 + - - +
459K GLU* 2.8 62.3 + - - +
601K HEM 3.9 22.9 - - + -
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Residues in contact with ALA 456 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319K THR* 3.8 22.0 - - - +
443K PHE* 4.5 1.3 - - + -
452K GLY 2.8 17.5 + - - +
453K ARG* 3.5 5.6 - - - +
455K LEU* 1.3 77.1 - - - +
457K GLU* 1.3 57.1 + - - +
459K GLU* 3.5 4.6 + - - +
460K MET* 3.0 37.0 + - - +
601K HEM 3.9 35.2 - - + +
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Residues in contact with GLU 457 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359K THR* 5.6 6.3 - - + -
366K ARG* 3.7 30.0 + - - +
369K LEU* 4.6 10.7 - - + +
370K LYS* 5.3 2.1 + - - -
440K HIS* 4.5 7.3 + - - -
443K PHE* 3.6 27.9 - - + -
453K ARG* 2.8 55.2 + - - +
454K ARG* 4.1 5.3 - - - +
456K ALA* 1.3 70.3 - - - +
458K ALA* 1.3 62.1 + - - +
460K MET* 4.4 6.9 - - - +
461K LEU* 3.0 33.0 + - + +
603K SO4 4.1 5.9 + - - +
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Residues in contact with ALA 458 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K VAL* 5.3 0.4 - - + -
157K PHE* 4.9 8.3 - - + -
158K LEU* 4.1 26.0 - - + -
161K VAL* 4.2 7.6 - - + -
359K THR* 5.4 5.5 - - + +
454K ARG 3.0 20.3 + - - +
455K LEU* 3.3 7.6 - - - +
457K GLU* 1.3 75.3 - - - +
459K GLU* 1.3 66.1 + - - +
461K LEU* 4.8 1.6 - - - -
462K LEU* 3.0 40.4 + - + +
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Residues in contact with GLU 459 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K VAL* 3.9 12.8 - - + +
195K TYR* 2.6 33.9 + - + +
196K THR* 4.0 8.0 - - - +
199K ALA* 3.7 22.8 - - + -
200K SER* 2.9 35.4 + - - -
315K SER* 5.8 0.4 - - - -
319K THR* 3.5 28.2 + - + +
323K LEU* 4.7 0.2 - - - -
455K LEU* 2.8 42.0 + - - +
456K ALA* 3.9 4.3 - - - +
458K ALA* 1.3 75.4 - - - +
460K MET* 1.3 62.1 + - - +
463K LEU* 3.4 8.1 + - - +
601K HEM 6.0 0.7 - - - -
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Residues in contact with MET 460 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319K THR* 3.8 23.1 - - + +
322K PRO* 3.5 33.9 - - + +
323K LEU* 3.9 20.6 - - + +
369K LEU* 3.3 42.4 - - + +
372K THR* 5.9 0.4 - - + -
373K LEU* 4.9 9.9 - - + -
443K PHE* 5.6 1.8 - - - -
456K ALA 3.0 23.7 + - - +
457K GLU* 4.4 3.8 - - - +
459K GLU* 1.3 75.8 - - - +
461K LEU* 1.3 62.5 + - - +
463K LEU* 4.1 1.4 - - - +
464K LEU* 3.4 31.4 + - + +
601K HEM 3.9 24.9 - - + -
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Residues in contact with LEU 461 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358K ALA* 3.3 36.8 - - + +
359K THR* 4.0 18.6 - - + -
362K LEU* 4.5 5.2 - - + +
365K LEU* 3.5 35.9 - - + +
366K ARG* 3.5 30.7 - - + +
369K LEU* 3.8 14.8 - - + -
457K GLU* 3.0 21.2 + - + +
458K ALA* 4.1 1.8 - - - +
460K MET* 1.3 76.5 - - - +
462K LEU* 1.3 61.1 + - + +
464K LEU* 3.6 0.6 + - - -
465K HIS* 2.9 30.5 + - - +
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Residues in contact with LEU 462 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K LEU* 3.3 31.0 - - + -
161K VAL* 3.4 21.5 - - + -
162K ASP* 3.1 27.4 - - - +
165K ALA* 3.8 16.4 - - + -
351K ILE* 4.9 4.3 - - + -
355K PRO 4.6 2.2 - - - +
358K ALA* 4.0 26.2 - - + -
458K ALA* 3.0 25.3 + - + +
459K GLU 4.4 0.9 - - - +
461K LEU* 1.3 74.1 - - + +
463K LEU* 1.3 66.4 + - - +
465K HIS* 3.4 4.8 + - + +
466K HIS* 3.0 32.8 + - + -
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Residues in contact with LEU 463 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K ALA* 3.8 9.9 - - - +
168K PHE* 3.4 42.0 - - + -
169K SER* 4.6 0.2 + - - -
192K ILE* 4.1 7.2 - - + -
195K TYR* 3.8 30.5 - - + +
323K LEU* 3.1 39.5 - - + -
327K LEU* 4.5 7.2 - - + -
459K GLU 3.4 17.7 + - - +
460K MET 4.1 0.9 - - - +
461K LEU 3.4 0.2 - - - -
462K LEU* 1.3 78.3 - - - +
464K LEU* 1.3 58.0 + - + +
466K HIS* 3.0 5.7 + - - +
467K VAL* 2.7 42.1 + - + +
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Residues in contact with LEU 464 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323K LEU* 4.7 5.2 - - + +
326K THR* 3.3 35.9 - - + -
327K LEU* 3.8 38.4 - - + -
330K LEU* 5.2 7.0 - - + -
365K LEU* 4.2 22.0 - - + -
368K ALA* 6.3 0.2 - - + -
369K LEU* 4.1 16.6 - - + -
460K MET* 3.4 21.1 + - + +
461K LEU* 4.0 2.7 - - - +
463K LEU* 1.3 86.4 - - + +
465K HIS* 1.3 63.3 + - - +
467K VAL* 4.3 4.5 - - + +
468K LEU* 3.0 34.9 + - + +
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Residues in contact with HIS 465 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344K SER* 3.3 40.1 + - - -
348K ALA* 4.4 4.1 + - - -
351K ILE* 3.3 47.0 - - + +
362K LEU* 4.0 6.7 - - + +
365K LEU* 4.0 14.0 - - + +
461K LEU 2.9 20.2 + - - +
462K LEU* 3.5 9.0 - - + +
463K LEU 3.2 0.2 - - - -
464K LEU* 1.3 79.7 - - - +
466K HIS* 1.3 84.7 + + - +
468K LEU* 3.9 2.5 - - - +
469K LYS* 3.3 42.8 + - + +
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Residues in contact with HIS 466 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162K ASP* 3.2 29.3 + - - -
165K ALA* 4.1 17.6 - - - +
166K ARG* 3.3 31.7 - - + +
169K SER* 3.2 15.9 + - - +
351K ILE* 5.3 2.9 - - + +
462K LEU* 3.0 29.1 + - + +
463K LEU 3.6 2.2 - - - +
465K HIS* 1.3 90.6 + + - +
467K VAL* 1.3 62.6 + - - +
469K LYS* 3.6 32.5 + - + -
470K HIS* 2.9 35.5 - - - -
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Residues in contact with VAL 467 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K PHE* 4.1 23.8 - - + -
169K SER* 3.6 12.8 - - - +
172K LEU* 5.2 1.1 - - + -
327K LEU* 4.2 10.5 - - + -
463K LEU* 2.7 31.8 + - + +
464K LEU* 3.4 8.0 + - + +
466K HIS* 1.3 71.7 - - - +
468K LEU* 1.3 63.8 + - + +
470K HIS 3.1 1.7 + - - -
471K PHE* 2.9 37.0 + - + +
473K VAL* 4.1 14.8 - - + -
499K PHE* 3.8 31.2 - - + -
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Residues in contact with LEU 468 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330K LEU* 4.1 15.5 - - + -
337K GLN* 3.9 30.1 - - + +
340K LEU* 3.9 24.9 - - + +
341K ARG* 3.3 56.5 + - + +
344K SER* 4.3 9.6 - - - +
365K LEU* 4.1 16.6 - - + -
464K LEU* 3.0 27.9 + - + +
465K HIS 3.9 2.9 - - - +
467K VAL* 1.3 80.3 - - + +
469K LYS* 1.3 60.5 + - - +
470K HIS 3.3 1.0 + - - -
471K PHE 3.7 4.1 + - - +
473K VAL* 5.9 2.9 - - + -
502K ILE* 5.2 0.3 - - - +
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Residues in contact with LYS 469 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341K ARG* 5.6 0.2 - - - -
344K SER* 4.3 14.1 - - - +
345K LEU* 4.2 26.7 - - + +
348K ALA* 4.3 18.4 + - + +
352K SER* 4.7 10.5 + - - -
465K HIS* 3.3 44.8 + - + +
466K HIS* 3.7 32.8 + - + +
467K VAL 3.3 0.2 - - - -
468K LEU* 1.3 79.2 - - - +
470K HIS* 1.3 81.8 + - + +
502K ILE* 4.6 10.7 - - - +
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Residues in contact with HIS 470 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K SER* 4.0 14.9 - - - -
173K LYS* 3.6 30.9 + - + +
466K HIS* 2.9 30.4 - - + -
467K VAL 3.1 2.4 + - - -
469K LYS* 1.3 108.9 + - + +
471K PHE* 1.3 90.0 + + + +
501K ALA* 3.5 0.7 - - - +
502K ILE* 3.1 31.8 + - - -
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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