Contacts of the helix formed by residues 536 - 549 (chain A) in PDB entry 1GGE
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 ARG 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLU* 5.5 2.6 + - - -
237A ASP* 2.9 45.1 + - - +
534A VAL* 3.5 7.1 - - - +
535A VAL* 1.3 71.8 - - - +
537A PRO* 1.3 72.0 - - - +
538A TYR* 3.3 35.0 - - + -
539A ILE* 3.1 23.7 + - + +
540A ARG* 3.7 0.7 + - - +
457B PRO* 5.3 5.1 - - - +
465B ILE* 3.5 34.9 + - - +
35D SER 4.3 8.1 - - - +
36D HIS 2.8 27.2 + - - -
38D PRO* 4.7 4.9 - - - +
49D PRO* 3.4 37.7 - - + +
50D THR 4.8 5.3 + - - -
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Residues in contact with PRO 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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535A VAL 3.0 12.3 - - - +
536A ARG* 1.3 84.0 - - + +
538A TYR* 1.3 63.7 + - + +
540A ARG* 2.9 42.9 + - + +
541A GLU* 3.1 21.2 + - + +
35D SER* 5.7 7.0 - - - +
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Residues in contact with TYR 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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536A ARG* 3.3 28.0 - - + -
537A PRO* 1.3 77.7 - - + +
539A ILE* 1.3 71.3 + - + +
541A GLU* 3.3 15.9 + - - +
542A ARG* 2.9 66.5 + - + +
464B SER* 2.6 30.2 + - - -
465B ILE* 4.0 2.9 - - - +
31D PRO* 3.4 36.8 - - + -
35D SER* 4.0 12.5 + - - +
36D HIS* 3.2 27.7 - - - +
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Residues in contact with ILE 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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237A ASP* 3.8 25.4 - - + +
240A TRP* 3.6 42.0 - - + +
241A ASP* 3.7 21.1 - - + +
244A SER* 4.7 2.2 - - - +
534A VAL* 3.7 7.4 - - + -
536A ARG* 3.1 34.8 + - + +
538A TYR* 1.3 97.7 - - + +
540A ARG* 1.3 67.9 + - - +
542A ARG* 3.2 7.4 + - - +
543A VAL* 3.0 21.0 + - + +
465B ILE* 4.5 2.0 - - + -
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Residues in contact with ARG 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.2 35.2 + - + +
532A SER 4.2 2.8 + - - -
534A VAL* 2.9 31.6 + - + -
535A VAL* 3.9 11.7 + - - +
536A ARG 4.1 5.8 - - - +
537A PRO* 2.9 31.0 + - - +
539A ILE* 1.3 79.3 - - - +
541A GLU* 1.3 57.0 + - - +
543A VAL* 3.2 2.8 + - - +
544A VAL* 2.9 32.9 + - - +
562A LEU* 4.2 28.1 + - + -
564A ILE* 4.3 7.0 - - + -
637D MET* 3.6 39.8 - - - +
638D GLY* 4.9 5.1 - - - +
650D ILE 5.5 1.0 + - - -
651D ALA 5.3 0.6 + - - -
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Residues in contact with GLU 541 (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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537A PRO* 3.1 16.8 + - + +
538A TYR* 3.6 18.8 - - - +
539A ILE 3.2 0.2 - - - -
540A ARG* 1.3 76.6 - - - +
542A ARG* 1.3 57.0 + - + +
544A VAL* 3.2 4.7 + - - +
545A ASP* 2.9 28.5 + - - +
564A ILE* 3.7 39.2 - - + +
570A GLN* 4.7 3.1 + - - -
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Residues in contact with ARG 542 (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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241A ASP* 4.9 1.2 + - - -
244A SER* 3.8 23.8 - - - +
245A LEU* 4.1 19.7 - - - +
538A TYR* 2.9 42.7 + - + +
539A ILE* 3.2 5.4 + - - +
541A GLU* 1.3 74.9 - - + +
543A VAL* 1.3 60.0 + - - +
545A ASP* 3.3 10.1 + - - +
546A GLN* 3.1 25.5 + - - +
464B SER* 3.7 16.6 - - - -
29D LEU* 2.9 30.9 + - - +
30D ALA 4.2 1.6 + - - -
31D PRO* 4.0 17.0 - - - +
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Residues in contact with VAL 543 (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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240A TRP* 3.8 54.5 - - + +
243A VAL* 5.0 4.7 - - + -
244A SER* 3.9 9.2 - - - +
250A LEU* 5.5 1.8 - - + -
527A PHE* 4.6 3.8 - - + -
531A LEU* 3.8 27.4 - - + -
539A ILE 3.0 14.7 + - - +
540A ARG 3.7 5.8 - - - +
542A ARG* 1.3 72.1 - - - +
544A VAL* 1.3 65.9 + - - +
546A GLN* 3.0 11.1 + - + +
547A LEU* 2.9 31.3 + - + +
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Residues in contact with VAL 544 (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 LEU* 4.6 2.0 - - + -
540A ARG 2.9 18.0 + - - +
541A GLU* 3.2 9.8 + - - +
543A VAL* 1.3 75.6 - - - +
545A ASP* 1.3 63.3 + - - +
547A LEU* 3.0 10.4 + - - +
548A ALA* 3.0 21.0 + - - +
555A ALA* 4.2 6.7 - - - +
558A VAL* 4.2 13.9 - - + -
559A ALA* 4.0 13.9 - - + -
562A LEU* 3.9 24.5 - - + -
564A ILE* 4.1 14.8 - - + -
566A LEU* 3.5 30.5 - - + -
570A GLN* 5.1 2.2 - - - +
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Residues in contact with ASP 545 (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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541A GLU 2.9 12.4 + - - +
542A ARG* 3.4 13.2 - - - +
544A VAL* 1.3 76.3 - - - +
546A GLN* 1.3 63.4 + - - +
548A ALA* 3.1 12.6 + - - +
549A HIS* 2.9 38.9 + - - -
570A GLN* 2.8 40.9 + - - +
573A ILE* 4.4 1.7 - - - +
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Residues in contact with GLN 546 (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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243A VAL 5.1 0.2 - - - +
244A SER* 3.3 29.1 + - - +
247A PRO* 3.6 24.5 - - - +
250A LEU* 3.6 22.2 - - + +
505A TYR* 2.6 37.0 + - - -
542A ARG 3.1 17.7 + - - +
543A VAL* 3.0 11.9 + - - +
545A ASP* 1.3 76.5 + - + +
547A LEU* 1.3 66.3 + - - +
549A HIS* 3.0 23.7 + - - +
550A ILE* 3.6 10.5 + - - +
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Residues in contact with LEU 547 (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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250A LEU* 4.8 7.6 - - + -
254A MET* 4.8 0.2 - - - -
527A PHE* 3.6 42.4 - - + -
543A VAL* 2.9 24.4 + - + +
544A VAL* 3.0 12.1 + - - +
546A GLN* 1.3 76.8 - - - +
548A ALA* 1.3 56.6 + - - +
550A ILE* 2.9 36.8 + - + +
551A ASP 3.1 15.8 + - - +
554A LEU* 4.3 10.4 - - + +
555A ALA* 3.7 14.6 - - - +
558A VAL* 3.9 41.1 - - + -
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Residues in contact with ALA 548 (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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544A VAL 3.0 11.9 + - - +
545A ASP* 3.1 13.4 + - - +
547A LEU* 1.3 76.2 - - - +
549A HIS* 1.3 58.7 + - - +
550A ILE 3.6 0.5 + - - -
551A ASP 4.4 1.3 + - - -
552A LEU* 3.1 31.7 - - + +
555A ALA* 3.5 16.3 - - + +
566A LEU* 4.9 4.0 - - + -
570A GLN* 4.2 16.2 - - + +
573A ILE* 3.8 24.8 - - + +
574A THR 5.9 0.2 - - - -
575A PRO* 5.9 0.7 - - - +
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Residues in contact with HIS 549 (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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505A TYR* 3.5 50.2 + + + +
545A ASP* 2.9 39.9 + - - -
546A GLN* 3.0 15.3 + - - +
548A ALA* 1.3 75.2 - - - +
550A ILE* 1.3 58.7 + - - +
573A ILE* 3.5 39.7 - - + +
574A THR 4.6 3.4 - - - +
575A PRO* 5.4 0.7 - - - -
576A PRO* 3.3 21.0 - - - +
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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