Contacts of the strand formed by residues 519 - 523 (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 THR 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A MET* 2.9 17.5 + - - +
391A ASN* 3.3 39.5 + - - +
392A ARG 3.4 5.4 + - - +
494A VAL* 3.7 18.3 - - + +
496A ILE* 5.4 7.0 - - + -
509A ALA* 5.5 5.2 - - - +
510A LEU* 5.4 5.4 + - - +
517A VAL* 2.7 19.4 + - - +
518A ASP* 1.3 70.9 + - - +
520A LEU* 1.3 72.1 + - - +
521A VAL* 5.5 3.8 - - + -
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Residues in contact with LEU 520 (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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380A ILE* 4.2 24.5 - - + -
390A MET* 4.6 7.9 - - + -
392A ARG* 3.7 32.3 - - + +
394A LEU* 4.0 25.4 - - + +
406A ALA* 4.9 7.6 - - + -
409A ALA* 4.6 10.3 - - + -
493A LEU* 5.4 4.7 - - + -
494A VAL 2.9 12.5 + - - +
495A ILE* 3.3 26.9 - - + -
496A ILE* 2.7 33.3 + - - +
519A THR* 1.3 77.2 - - - +
521A VAL* 1.3 63.3 + - - +
522A MET* 5.0 2.2 - - - +
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Residues in contact with VAL 521 (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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392A ARG 3.3 6.3 - - - +
393A LEU* 2.9 42.4 - - + +
394A LEU 2.7 23.5 + - - -
496A ILE* 3.7 25.6 - - + -
498A GLU* 4.9 5.2 - - - +
519A THR* 5.5 4.0 - - + -
520A LEU* 1.3 80.6 - - - +
522A MET* 1.3 59.7 + - - +
523A SER* 5.8 0.9 - - - -
539A LEU* 3.7 9.9 - - + -
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Residues in contact with MET 522 (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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394A LEU* 3.0 27.6 - - + +
402A LYS* 4.8 10.5 - - + -
403A THR* 4.8 8.3 - - + +
406A ALA* 4.2 22.7 - - + -
422A PHE* 4.5 9.6 - - + -
433A HIS* 4.6 4.0 - - + +
495A ILE* 4.5 12.8 - - + -
496A ILE 2.9 19.3 + - - +
497A ASP* 2.6 35.6 - - - +
498A GLU* 3.5 26.1 + - - +
520A LEU* 5.9 2.9 - - + -
521A VAL* 1.3 76.8 - - - +
523A SER* 1.3 62.0 + - - +
1757A MG 2.8 28.5 - - - -
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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
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393A LEU* 4.4 17.9 - - - -
394A LEU 3.0 8.1 + - - -
395A GLN* 3.9 10.6 - - - +
396A GLY 3.3 26.5 + - - +
402A LYS* 3.3 8.3 + - - +
498A GLU* 3.5 15.4 + - - -
499A GLN* 4.3 5.7 + - - -
521A VAL* 5.8 0.4 - - - -
522A MET* 1.3 77.1 - - - +
524A ALA* 1.3 60.5 + - - +
525A THR* 3.9 16.6 + - - -
527A ILE* 6.1 0.6 - - - +
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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