Contacts of the helix formed by residues 527 - 540 (chain A) in PDB entry 6S1M
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 MET 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A LEU 3.9 4.6 + - - -
524A GLU 3.9 7.5 + - - +
525A ARG 3.2 5.8 - - - +
526A LEU* 1.3 78.6 - - - +
528A VAL* 1.3 63.7 - - - +
529A LEU 3.6 0.9 - - - -
530A VAL* 4.4 24.7 - - + +
531A ASN* 3.0 46.3 + - - +
682A ARG* 4.9 9.2 - - - +
685A VAL* 3.7 28.5 - - + +
686A LEU* 3.8 24.5 - - + -
689A ARG* 4.9 7.2 - - - +
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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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457A MET* 3.8 28.5 - - + -
459A MET* 4.0 24.7 - - + -
462A VAL* 4.3 19.5 - - + -
523A LEU* 3.5 26.4 + - + +
526A LEU* 3.9 21.5 - - + +
527A MET* 1.3 76.7 - - - +
529A LEU* 1.3 60.5 - - - +
531A ASN* 3.2 6.3 + - - +
532A ALA* 2.9 25.6 + - + +
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Residues in contact with LEU 529 (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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307A ILE* 5.9 4.9 - - + -
310A LEU* 4.6 21.1 - - + -
312A VAL* 4.9 12.1 - - + -
344A TRP* 4.6 28.9 - - + +
392A VAL* 5.3 9.6 - - + -
457A MET* 4.9 13.0 - - - -
523A LEU* 4.0 29.7 + - + +
527A MET 3.6 0.2 - - - -
528A VAL* 1.3 77.8 - - - +
530A VAL* 1.3 62.6 + - + +
532A ALA* 3.3 7.9 + - + +
533A VAL* 3.0 43.5 + - + +
543A LEU* 5.6 7.2 - - + -
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Residues in contact with VAL 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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307A ILE* 4.9 11.2 - - + -
344A TRP* 3.8 32.8 - - + -
527A MET* 4.7 24.9 - - + +
528A VAL 3.4 0.2 - - - -
529A LEU* 1.3 76.7 - - + +
531A ASN* 1.3 63.5 + - - +
533A VAL* 3.5 6.4 + - - +
534A GLU* 3.0 30.5 + - + +
689A ARG* 6.3 0.4 - - - +
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Residues in contact with ASN 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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526A LEU 4.7 3.2 + - - -
527A MET* 3.0 38.5 + - - +
528A VAL* 3.2 5.4 + - - +
530A VAL* 1.3 79.2 - - - +
532A ALA* 1.3 59.2 + - - +
534A GLU* 3.8 6.2 - - - +
535A MET* 2.9 31.4 + - - +
685A VAL* 4.6 6.5 + - - +
688A GLY 5.5 0.2 - - - -
689A ARG* 3.3 45.7 + - + +
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Residues in contact with ALA 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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457A MET* 5.4 13.0 - - + -
528A VAL* 2.9 14.0 + - + +
529A LEU* 3.3 13.0 + - + +
531A ASN* 1.3 78.3 - - - +
533A VAL* 1.3 57.2 + - + +
535A MET* 3.4 5.9 + - - +
536A ALA* 3.0 28.9 + - - +
543A LEU* 3.8 15.5 - - + +
546A LEU* 3.7 13.9 - - + +
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Residues in contact with VAL 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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262A GLY 5.0 0.2 - - - +
263A CYS* 4.4 22.0 - - + -
307A ILE* 4.8 20.4 - - + -
310A LEU* 6.2 0.9 - - + -
529A LEU* 3.0 37.8 + - + +
530A VAL* 3.9 6.1 - - - +
532A ALA* 1.3 74.2 - - + +
534A GLU* 1.3 59.2 + - - +
536A ALA* 3.3 3.4 + - - +
537A ARG* 3.0 59.7 + - - +
543A LEU* 4.5 9.9 - - + -
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Residues in contact with GLU 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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530A VAL* 3.0 18.4 + - + +
531A ASN* 3.9 5.9 - - - +
533A VAL* 1.3 77.4 - - - +
535A MET* 1.3 57.9 + - - +
537A ARG* 3.3 7.4 + - + +
538A VAL* 3.0 40.1 + - + +
666A ALA* 5.4 2.9 - - - +
669A ARG* 5.6 5.5 + - - +
689A ARG* 2.4 48.9 + - - +
693A LEU* 3.8 25.8 - - - +
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Residues in contact with MET 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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531A ASN 2.9 19.6 + - - +
532A ALA* 3.7 5.2 - - - +
534A GLU* 1.3 77.2 - - - +
536A ALA* 1.3 52.2 + - - +
538A VAL* 3.4 3.0 + - + -
539A THR* 2.6 65.9 + - + +
546A LEU* 3.8 23.6 - - + -
554A LYS* 4.2 10.5 - - - +
663A LEU* 5.3 2.2 - - + -
692A ALA* 5.0 14.1 - - - -
693A LEU* 4.2 25.4 - - + -
696A SER* 3.4 26.9 - - - +
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Residues in contact with ALA 536 (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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262A GLY* 3.6 23.8 + - - +
263A CYS* 4.8 0.4 - - - -
532A ALA 3.0 17.4 + - - +
533A VAL* 3.8 4.9 - - - +
535A MET* 1.3 76.9 - - - +
537A ARG* 1.3 59.2 + - - +
539A THR* 4.0 3.8 - - - -
540A GLY* 3.2 23.4 + - - -
541A VAL* 3.5 19.2 - - - +
542A PRO 4.5 4.5 - - - +
543A LEU* 4.1 17.7 - - + -
546A LEU* 4.1 5.9 - - + +
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Residues in contact with ARG 537 (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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97A GLN* 3.1 22.0 - - - +
261A VAL* 4.4 13.1 - - + +
262A GLY 3.6 15.7 - - - +
263A CYS 3.3 14.7 + - - +
265A TRP* 4.8 1.6 - - - +
300A PRO* 3.7 42.0 - - + +
304A TRP 4.0 2.9 + - - -
305A GLN* 3.7 31.7 + - - +
306A ARG 3.0 20.6 + - - -
307A ILE* 4.6 2.9 - - - +
533A VAL* 3.0 39.3 + - + +
534A GLU* 3.9 6.7 - - + +
535A MET 3.2 0.2 - - - -
536A ALA* 1.3 79.0 - - - +
538A VAL* 1.3 64.4 + - + +
540A GLY 4.3 2.6 + - - -
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Residues in contact with VAL 538 (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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534A GLU* 3.0 36.3 + - + +
535A MET* 4.2 4.0 - - + +
537A ARG* 1.3 80.2 - - + +
539A THR* 1.3 66.9 + - + +
558A GLN* 3.8 7.0 + - - +
662A ASN* 4.5 21.0 + - - +
663A LEU* 4.4 23.8 - - + -
666A ALA* 4.7 20.2 - - + -
669A ARG* 5.6 5.8 - - - +
693A LEU* 4.8 8.3 - - + -
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Residues in contact with THR 539 (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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535A MET* 2.6 47.4 + - + +
536A ALA* 4.0 0.2 - - - -
538A VAL* 1.3 82.1 - - + +
540A GLY* 1.3 60.1 + - - +
541A VAL* 3.5 20.9 - - - +
554A LYS* 3.8 29.0 - - + -
557A SER* 3.8 9.9 + - - -
558A GLN* 3.4 38.6 - - - +
561A ARG* 4.3 5.1 + - - -
663A LEU* 5.7 1.6 - - + -
696A SER* 5.6 1.3 - - - +
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Residues in contact with GLY 540 (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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252A ILE* 5.6 2.4 - - - +
255A MET* 4.4 7.3 - - - +
261A VAL* 4.1 14.4 - - - -
262A GLY 4.5 2.7 - - - -
536A ALA 3.2 15.3 + - - -
537A ARG 4.3 1.2 + - - -
538A VAL 3.7 1.6 - - - -
539A THR* 1.3 77.8 - - - +
541A VAL* 1.3 62.7 + - - +
542A PRO* 4.5 0.3 - - - +
557A SER* 3.7 5.7 + - - -
561A ARG* 3.0 33.8 + - - -
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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