Contacts of the helix formed by residues 518 - 536 (chain A) in PDB entry 6J95
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 518 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.3 2.2 - - - -
516A CYS* 3.0 14.3 - - - -
517A ILE* 1.3 81.3 - - - +
519A ASP* 1.3 56.5 + - - +
520A MET 3.4 2.2 - - - -
521A PHE* 3.4 12.4 - - - +
522A ALA* 2.8 34.0 + - - +
601A HEM 3.8 23.7 - - - +
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Residues in contact with ASP 519 (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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509A PHE* 3.6 43.4 - - + -
515A LYS* 3.7 21.3 + - - +
516A CYS* 3.4 16.7 - - - +
517A ILE* 3.9 6.2 - - - +
518A GLY* 1.3 75.8 - - - +
520A MET* 1.3 74.3 + - - +
523A SER* 2.7 37.3 + - - -
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Residues in contact with MET 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 4.8 14.8 - - + -
517A ILE 5.2 0.2 + - - -
518A GLY 3.4 0.2 - - - -
519A ASP* 1.3 97.4 + - - +
521A PHE* 1.3 66.7 + - - +
523A SER* 3.3 6.3 + - - -
524A PHE* 3.0 63.4 + - + -
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Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.4 12.1 - - + +
212A TYR* 3.7 22.0 - + - -
213A VAL* 4.5 17.7 - - + +
216A MET* 3.7 18.8 - - + -
220A PHE* 3.5 26.4 - + - -
254A ILE* 4.4 2.5 - - + -
255A ILE* 4.2 12.8 - - + -
258A ALA* 3.5 32.8 - - + -
518A GLY* 3.4 16.1 - - - +
520A MET* 1.3 78.1 - - - +
522A ALA* 1.3 57.8 + - - +
525A GLU* 2.9 49.4 + - - +
601A HEM 3.5 30.7 - - + -
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER* 4.1 4.3 - - - +
509A PHE* 4.1 6.5 - - + -
518A GLY 2.8 20.4 + - - +
521A PHE* 1.3 76.8 - - - +
523A SER* 1.3 65.7 + - - +
525A GLU* 3.6 6.2 - - - +
526A ASN* 2.8 31.9 + - - +
601A HEM 3.4 45.5 - - + -
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A MET* 3.3 27.7 - - - +
509A PHE* 3.6 19.1 - - - -
519A ASP 2.7 23.5 + - - -
520A MET* 3.3 10.5 + - - -
522A ALA* 1.3 76.6 - - - +
524A PHE* 1.3 69.5 + - - +
527A VAL* 3.1 28.7 + - - +
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Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 3.5 28.5 - - + -
217A ILE* 3.8 13.9 - - + -
220A PHE* 4.1 11.0 - - + -
418A ILE* 3.7 20.9 - - + -
421A MET* 3.5 43.5 - - + +
520A MET* 3.0 45.3 + - + +
521A PHE 3.9 2.0 - - - +
523A SER* 1.3 78.6 - - - +
525A GLU* 1.3 67.8 + - - +
527A VAL* 3.2 3.8 + - + +
528A VAL* 2.9 28.1 + - - +
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Residues in contact with GLU 525 (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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220A PHE* 3.4 22.1 - - + +
224A SER* 5.2 0.2 + - - -
251A THR* 3.9 21.6 - - + +
254A ILE* 3.5 44.1 - - + +
255A ILE* 5.6 0.9 - - - +
378A GLY 4.6 6.6 - - - +
382A SER* 3.9 19.0 + - - +
386A LEU* 6.1 1.6 - - + -
521A PHE* 2.9 39.0 + - - +
522A ALA* 3.3 6.6 + - - +
524A PHE* 1.3 76.3 - - - +
526A ASN* 1.3 64.7 + - - +
528A VAL* 3.3 2.8 + - - +
529A ALA* 3.1 22.8 + - + +
601A HEM 4.8 0.7 - - - +
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Residues in contact with ASN 526 (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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382A SER* 3.0 33.8 + - - +
385A VAL* 4.0 13.9 - - + +
386A LEU* 3.3 32.6 - - + +
431A MET* 4.0 20.3 - - + -
435A LEU* 5.8 0.6 - - - +
522A ALA 2.8 29.5 + - - +
525A GLU* 1.3 74.1 - - - +
527A VAL* 1.3 66.8 + - - +
529A ALA* 3.9 0.6 - - - +
530A ILE* 2.9 35.2 + - + +
601A HEM 3.8 12.5 - - - +
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Residues in contact with VAL 527 (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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421A MET* 4.1 17.3 - - - +
424A LEU* 3.7 32.8 - - + -
427A THR* 3.7 18.1 - - + +
428A THR* 3.9 33.4 - - + +
431A MET* 4.1 11.7 - - + -
523A SER 3.1 20.2 + - - +
524A PHE* 3.2 6.0 + - + +
526A ASN* 1.3 75.9 - - - +
528A VAL* 1.3 63.1 + - - +
530A ILE* 4.7 0.9 - - - -
531A ALA* 3.0 23.9 + - - +
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Residues in contact with VAL 528 (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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217A ILE* 4.3 10.8 - - + +
220A PHE* 3.8 20.4 - - + +
221A GLY* 3.7 32.3 - - - +
224A SER* 4.1 1.8 - - - +
416A PRO* 3.9 26.2 - - + -
421A MET* 3.7 23.3 - - + -
524A PHE 2.9 21.5 + - - +
525A GLU 3.7 4.5 - - - +
527A VAL* 1.3 76.9 - - - +
529A ALA* 1.3 64.1 + - - +
531A ALA* 3.9 0.6 - - - +
532A MET* 3.0 27.2 + - - +
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Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.6 21.9 + - - +
247A PHE* 5.4 1.6 - - + -
250A LEU* 4.2 10.3 - - + -
386A LEU* 3.9 29.8 - - + -
390A PHE* 5.3 1.3 - - - -
525A GLU* 3.1 17.0 + - + +
526A ASN 3.9 3.4 - - - +
528A VAL* 1.3 76.4 - - - +
530A ILE* 1.3 63.5 + - - +
532A MET 4.0 0.2 - - - -
533A LEU* 3.1 33.0 + - + +
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Residues in contact with ILE 530 (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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385A VAL* 5.9 0.2 - - + -
386A LEU* 3.9 17.0 - - + -
389A THR* 3.8 32.3 - - + +
390A PHE* 4.2 13.9 - - + -
393A LEU* 5.0 0.4 - - + -
403A LEU* 3.9 24.0 - - + -
427A THR* 3.9 15.9 - - + -
430A VAL* 4.7 3.6 - - + -
431A MET* 4.2 24.9 - - + +
526A ASN* 2.9 27.8 + - + +
527A VAL* 3.9 4.5 - - - +
529A ALA* 1.3 76.2 - - - +
531A ALA* 1.3 64.1 + - - +
533A LEU* 3.9 0.3 - - - +
534A ILE* 2.9 33.9 + - + +
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Residues in contact with ALA 531 (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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407A VAL* 3.8 24.0 - - + +
411A ILE* 3.7 21.5 - - + -
416A PRO* 5.0 0.9 - - + -
424A LEU* 4.0 16.8 - - + -
427A THR* 4.3 3.8 - - + -
527A VAL 3.0 18.4 + - - +
528A VAL* 3.9 3.4 - - - +
530A ILE* 1.3 79.4 - - - +
532A MET* 1.3 57.4 + - - +
534A ILE* 3.9 0.6 - - - -
535A ARG* 2.9 30.7 + - - +
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Residues in contact with MET 532 (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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221A GLY* 3.7 33.9 - - - +
224A SER* 4.0 11.2 - - - -
225A ASP* 4.0 16.4 - - + -
228A CYS* 4.2 8.1 - - - -
411A ILE* 4.7 3.1 - - + -
414A ARG 4.4 7.2 - - - +
415A PHE* 4.0 15.3 - - + +
416A PRO* 3.7 31.2 - - + -
528A VAL* 3.0 19.2 + - - +
529A ALA 4.2 1.6 - - - +
531A ALA* 1.3 76.4 - - - +
533A LEU* 1.3 63.3 + - - +
535A ARG* 4.4 0.4 - - - -
536A ARG* 2.9 64.2 + - - +
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Residues in contact with LEU 533 (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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224A SER* 4.4 6.7 - - - +
227A LEU* 4.2 15.9 - - + -
228A CYS* 3.6 22.7 - - - -
231A LEU* 3.9 26.5 - - + -
243A MET* 4.1 2.9 - - + -
247A PHE* 3.7 25.8 - - + -
390A PHE* 3.7 29.2 - - + -
529A ALA* 3.1 27.3 + - + +
532A MET* 1.3 76.8 - - + +
534A ILE* 1.3 60.7 + - - +
536A ARG 3.1 1.9 + - - -
537A PHE* 3.0 33.6 + - - +
539A PHE* 3.9 10.3 - - + -
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Residues in contact with ILE 534 (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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390A PHE* 3.7 27.1 - - + -
393A LEU* 3.8 14.8 - - + -
400A VAL* 4.9 10.5 - - + +
403A LEU* 3.7 35.4 - - + -
404A GLN* 3.7 28.5 - - + +
407A VAL* 4.2 4.7 - - + -
530A ILE* 2.9 22.4 + - + +
531A ALA* 4.1 2.5 - - - +
533A LEU* 1.3 72.2 - - - +
535A ARG* 1.3 65.2 + - - +
537A PHE 3.6 5.5 - - - +
539A PHE* 4.3 11.9 - - + -
569A ARG* 3.3 22.5 + - - -
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Residues in contact with ARG 535 (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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407A VAL* 3.9 11.1 - - + +
408A ASP* 2.8 48.2 + - - +
411A ILE* 5.0 1.1 - - + -
412A GLY* 3.2 35.0 - - - +
413A ASP* 2.8 35.4 + - - +
531A ALA 2.9 18.4 + - - +
532A MET* 3.7 6.3 - - - +
533A LEU 3.2 0.2 - - - -
534A ILE* 1.3 78.4 - - - +
536A ARG* 1.3 76.0 + - + +
569A ARG* 2.9 26.9 + - - +
570A THR* 3.8 24.1 - - - +
577A SER* 4.1 13.3 - - - -
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Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 4.6 8.3 + - - -
228A CYS* 3.7 24.7 - - - +
232A ASP* 5.9 0.2 - - - +
411A ILE* 5.7 0.4 - - - +
412A GLY 4.6 2.2 + - - -
413A ASP* 3.2 38.7 + - - +
414A ARG 5.2 0.4 + - - -
415A PHE* 6.2 0.2 - - - -
532A MET* 2.9 59.7 + - - +
533A LEU 3.1 2.0 + - - -
535A ARG* 1.3 98.1 - - + +
537A PHE* 1.3 81.3 + - + +
568A LYS* 3.6 2.6 + - - +
569A ARG* 2.7 29.2 + - - +
570A THR* 4.1 15.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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