Contacts of the helix formed by residues 528 - 536 (chain A) in PDB entry 1GM5
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 PRO 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A ILE* 1.3 92.0 - - + +
529A ARG* 1.3 61.9 + - - +
530A SER* 4.8 3.1 - - - +
531A MET* 3.1 17.2 + - + +
532A ALA 2.9 23.2 + - - -
544A ILE* 5.9 0.2 - - + -
715A PHE* 4.7 9.4 - - + +
718A ALA* 3.2 28.0 - - + -
719A GLU* 3.1 29.4 - - + +
722A LEU* 4.1 22.9 - - + -
729A GLU* 5.7 2.7 - - - +
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Residues in contact with ARG 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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527A ILE 3.7 0.8 + - - -
528A PRO* 1.3 67.9 - - - +
530A SER* 1.3 69.1 + - - +
532A ALA* 2.9 9.2 + - + +
533A LEU* 2.3 83.6 + - + +
544A ILE* 5.3 11.5 - - + +
747A TYR* 5.0 14.2 + - - -
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Residues in contact with SER 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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528A PRO* 4.8 2.8 - - - +
529A ARG* 1.3 82.8 - - - +
531A MET* 1.3 69.8 + - - +
533A LEU* 3.1 9.8 + - - +
534A ALA* 3.0 22.3 + - - +
722A LEU* 4.2 4.9 - - - +
741A PHE* 2.5 43.9 - - - -
743A VAL* 4.3 19.5 - - - -
746A LEU* 4.0 7.3 - - - +
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Residues in contact with MET 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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527A ILE* 3.7 25.6 - - + -
528A PRO* 3.1 17.1 + - + +
530A SER* 1.3 81.2 + - - +
532A ALA* 1.3 70.8 + - - +
534A ALA* 4.3 2.2 - - - -
535A PHE* 2.8 76.0 + - + +
536A TYR* 4.0 7.0 + - + +
722A LEU* 5.0 7.2 - - + -
727A PRO* 3.9 26.5 - - + -
729A GLU* 4.3 31.2 - - + +
741A PHE* 4.7 7.2 - - + -
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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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393A LEU* 6.2 0.9 - - + -
395A GLN* 5.4 1.8 - - - +
527A ILE* 3.4 15.1 - - + +
528A PRO 2.9 13.1 + - - +
529A ARG* 2.9 16.3 + - + +
531A MET* 1.3 81.9 - - - +
533A LEU* 1.3 59.6 + - + +
534A ALA 2.9 2.1 + - - -
536A TYR* 3.0 14.6 + - - +
537A GLY* 2.7 27.1 + - - -
542A THR* 4.5 21.3 - - + +
544A ILE* 6.2 0.4 - - + -
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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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333A GLN* 3.4 22.3 + - - -
336A PHE* 6.1 0.2 - - - -
529A ARG* 2.3 68.3 + - + +
530A SER* 3.8 5.2 - - - +
532A ALA* 1.3 74.6 - - + +
534A ALA* 1.3 56.6 + - - +
537A GLY* 3.6 25.4 - - - +
539A LEU 6.1 0.7 - - - +
540A ASP 5.8 4.5 - - - +
541A VAL* 6.1 2.0 - - - -
542A THR* 5.7 6.3 - - + -
746A LEU* 4.2 8.0 - - + +
747A TYR* 5.4 9.6 - - + -
750A LEU* 5.1 14.8 - - + -
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Residues in contact with ALA 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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329A LEU* 5.5 5.4 - - + +
332A LEU* 2.7 29.6 - - - +
333A GLN* 4.9 2.7 - - - +
336A PHE* 4.2 4.5 - - - -
530A SER 3.0 20.0 - - - +
531A MET* 4.1 3.6 - - - +
532A ALA 2.9 1.2 + - - -
533A LEU* 1.3 76.2 - - - +
535A PHE* 1.3 71.9 + - + +
536A TYR 3.6 0.2 - - - -
736A HIS* 6.1 2.0 - - + -
741A PHE* 5.3 3.4 - - + -
746A LEU* 3.1 32.2 - - + +
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Residues in contact with PHE 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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332A LEU* 3.7 19.5 - - + +
336A PHE* 3.1 16.3 - - - -
531A MET* 2.8 69.0 + - + +
534A ALA* 1.3 79.7 - - + +
536A TYR* 1.3 84.9 + - + +
727A PRO* 4.6 14.1 - - + -
736A HIS* 3.8 41.1 - + + -
741A PHE* 5.3 6.5 - + - -
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Residues in contact with TYR 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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336A PHE* 1.7 38.6 - - - -
393A LEU* 5.9 8.3 - - + -
527A ILE* 4.0 28.6 - - + +
531A MET* 5.0 8.4 - - + +
532A ALA* 3.0 13.6 + - - +
535A PHE* 1.3 101.7 - - + +
537A GLY* 1.3 52.8 - - - +
538A ASP* 2.1 15.5 + - - +
539A LEU* 4.1 20.2 - - + -
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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