Contacts of the helix formed by residues 540 - 551 (chain D) in PDB entry 1S77
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 CYS 540 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538D GLY 3.5 1.6 + - - -
539D SER* 1.3 75.2 - - - +
541D SER* 1.3 66.8 + - - +
542D GLY* 3.0 5.5 + - - -
543D ILE* 3.1 36.1 + - - +
544D GLN* 3.2 8.1 + - - +
559D VAL* 4.1 8.3 - - + -
570D ILE* 4.2 9.9 - - + -
571D TYR* 3.2 34.5 - - + +
634D VAL 5.4 0.2 - - - -
635D MET* 4.7 12.6 - - - -
812D ASP* 5.3 0.2 + - - -
901D POP 2.7 21.8 + - - +
1R 3DA 5.6 4.5 - - - -
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Residues in contact with SER 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D GLY* 4.6 4.8 + - - -
539D SER 3.5 2.0 - - - +
540D CYS* 1.3 71.2 - - - +
542D GLY* 1.3 66.8 + - - +
544D GLN* 3.5 18.4 - - - -
545D HIS* 2.9 46.6 + - - -
787D ASP* 5.0 3.9 - - - +
812D ASP* 3.6 25.4 + - - +
883D ALA* 5.2 3.4 - - - -
1R 3DA 3.4 27.0 + - - +
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Residues in contact with GLY 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D CYS* 3.0 3.9 + - - -
541D SER* 1.3 83.2 + - - +
543D ILE* 1.3 61.9 + - - +
545D HIS* 3.4 3.8 + - - +
546D PHE* 3.1 27.1 + - - -
635D MET* 5.8 2.0 - - - -
639D TYR* 3.2 31.1 + - - -
783D VAL* 3.9 8.6 - - - +
1R 3DA 4.1 7.1 + - - +
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Residues in contact with ILE 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D CYS* 3.1 22.7 + - - +
542D GLY* 1.3 73.6 - - - +
544D GLN* 1.3 68.3 + - - +
546D PHE* 3.0 5.3 + - + -
547D SER* 2.7 39.5 + - - +
555D GLY* 4.6 10.1 - - - +
559D VAL* 3.6 22.7 - - + -
570D ILE* 4.2 16.2 - - + -
634D VAL 4.6 9.6 - - - +
635D MET 5.3 4.5 - - - +
638D ALA* 4.1 16.6 - - + -
689D VAL* 3.7 32.8 - - + -
692D ALA* 4.3 5.2 - - + -
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Residues in contact with GLN 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D GLY* 4.1 0.2 - - - -
539D SER* 2.8 39.0 + - - +
540D CYS 3.3 14.8 - - - +
541D SER* 3.1 13.2 + - - +
543D ILE* 1.3 78.6 - - - +
545D HIS* 1.3 57.7 + - - +
547D SER 3.0 0.2 + - - -
548D ALA* 2.8 28.4 + - - +
559D VAL* 2.9 34.5 + - + +
561D LEU* 3.4 24.9 - - + +
832D MET* 4.2 9.5 - - + +
881D ALA* 3.7 7.9 + - - +
883D ALA* 3.9 32.2 - - - +
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Residues in contact with HIS 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D SER* 2.9 39.7 + - - +
542D GLY 3.7 3.8 - - - +
544D GLN* 1.3 75.7 - - - +
546D PHE* 1.3 62.9 + - - +
548D ALA* 3.8 4.1 - - - +
549D MET* 3.0 34.6 + - + +
783D VAL* 4.0 18.2 - - + -
786D GLN* 3.8 6.5 + - + -
787D ASP* 3.3 42.5 - - + +
790D HIS* 3.9 20.9 - + + -
832D MET* 4.0 19.7 - - + +
836D TYR* 2.6 30.0 + + - +
883D ALA* 5.6 0.8 + - - +
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Residues in contact with PHE 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542D GLY 3.1 20.2 + - - -
543D ILE* 3.0 10.8 + - + +
545D HIS* 1.3 76.7 - - - +
547D SER* 1.3 63.8 + - - +
549D MET* 3.3 13.9 - - + +
550D LEU* 3.0 31.1 + - - +
638D ALA* 3.4 39.7 - - + -
639D TYR* 4.4 7.4 - + - -
692D ALA* 3.6 32.8 - - + -
695D ALA* 3.9 26.9 - - + -
696D MET* 4.5 8.1 - - - -
699D LEU* 4.5 11.7 - - + -
779D ALA* 4.9 2.5 - - + -
783D VAL* 3.5 30.5 - - + -
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Residues in contact with SER 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D ILE* 2.7 40.7 + - - +
544D GLN 3.4 3.1 - - - -
546D PHE* 1.3 73.1 - - - +
548D ALA* 1.3 52.3 + - - +
551D ARG* 2.5 33.6 + - - -
552D ASP* 2.8 23.7 + - - +
555D GLY* 3.5 2.9 - - - -
556D GLY* 3.3 30.1 + - - -
559D VAL* 4.1 0.7 - - - +
561D LEU* 3.6 11.7 - - - -
870D LEU* 3.7 2.0 - - - +
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Residues in contact with ALA 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D GLN 2.8 19.7 + - - +
545D HIS* 3.8 2.9 - - - +
547D SER* 1.3 72.8 - - - +
549D MET* 1.3 59.2 - - - +
551D ARG* 2.9 31.4 + - - -
561D LEU* 4.0 6.2 - - + +
832D MET* 5.0 5.4 - - + -
836D TYR* 3.4 33.0 - - + +
870D LEU* 4.3 2.7 - - - -
872D LEU* 3.7 22.1 - - + +
875D ILE* 5.1 3.1 - - + -
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Residues in contact with MET 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D HIS* 3.0 25.1 + - + +
546D PHE* 3.3 26.2 - - + +
548D ALA* 1.3 77.9 - - - +
550D LEU* 1.3 66.5 + - + +
551D ARG* 4.8 1.5 - - - +
782D PHE* 3.9 15.5 - - + -
783D VAL* 5.3 3.1 - - + -
786D GLN* 4.1 15.9 - - + -
836D TYR* 3.6 27.0 - - + +
839D CYS 6.0 0.9 - - - -
840D ASP* 4.7 5.8 - - - +
841D VAL* 3.5 21.8 - - + +
842D LEU* 3.3 37.1 - - + +
867D LYS* 4.0 16.3 - - - +
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Residues in contact with LEU 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D PHE 3.0 21.3 + - - +
547D SER 4.0 1.6 - - - +
549D MET* 1.3 83.5 - - + +
551D ARG* 1.3 65.3 + - - +
552D ASP* 3.1 9.3 + - + +
691D ALA* 3.2 45.8 - - + +
692D ALA* 3.9 3.4 - - - +
695D ALA* 3.5 13.7 - - + +
842D LEU* 3.5 19.5 - - + -
865D PRO* 3.5 34.1 - - + -
866D ALA 4.2 5.2 - - - +
867D LYS* 3.5 12.8 - - - +
868D GLY 2.9 23.4 + - - -
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Residues in contact with ARG 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D SER 2.5 14.2 + - - -
548D ALA 2.9 10.2 + - - +
549D MET 4.8 1.3 - - - +
550D LEU* 1.3 77.4 - - - +
552D ASP* 1.3 58.3 + - - -
553D GLU 3.2 0.2 + - - -
836D TYR 3.4 17.7 + - - -
837D GLU* 4.1 14.6 + - - +
867D LYS* 4.5 20.0 - - + +
868D GLY* 3.1 26.7 + - - +
870D LEU* 2.8 42.3 + - - +
872D LEU* 2.9 39.7 - - - +
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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