Contacts of the helix formed by residues 519 - 528 (chain A) in PDB entry 1V9P
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 GLY 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A TYR* 4.1 6.1 - - - -
517A GLY 2.6 12.0 + - - -
518A VAL* 1.3 73.4 - - - +
520A GLU* 1.3 59.3 + - - -
521A VAL* 2.9 7.3 + - - -
522A LEU* 3.3 9.7 - - - +
523A ALA* 2.7 36.6 + - - +
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Residues in contact with GLU 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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445A LYS* 4.0 33.8 + - + +
511A TYR* 3.7 35.8 - - + +
519A GLY* 1.3 71.5 - - - +
521A VAL* 1.3 60.1 + - - +
523A ALA* 3.8 2.4 - - - +
524A ARG* 2.9 49.4 + - - +
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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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519A GLY* 4.7 3.4 - - - -
520A GLU* 1.3 78.7 - - - +
522A LEU* 1.3 69.4 + - + +
523A ALA 3.0 4.9 + - - -
524A ARG* 3.3 7.1 + - + +
525A ASN* 2.9 43.6 + - - +
548A GLU* 5.4 1.3 - - - +
549A GLU* 4.1 28.7 - - - +
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Residues in contact with LEU 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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517A GLY 4.1 6.7 - - - +
518A VAL* 3.7 18.6 - - + +
519A GLY* 3.0 18.3 + - - +
521A VAL* 1.3 86.2 - - + +
523A ALA* 1.3 59.9 + - - +
525A ASN* 3.9 5.5 + - + +
526A LEU* 3.3 31.1 + - + +
548A GLU 3.9 9.2 - - - +
549A GLU* 3.6 27.1 - - + +
550A VAL* 3.3 35.4 - - + -
554A THR* 5.9 3.4 - - - +
558A ILE* 4.3 7.6 - - + -
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Residues in contact with ALA 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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507A GLU* 3.9 20.4 - - - +
510A LEU* 3.9 7.2 - - + +
511A TYR* 3.9 17.5 - - + +
518A VAL* 3.3 19.9 - - + +
519A GLY 2.7 20.5 + - - +
520A GLU 3.8 5.6 - - - +
522A LEU* 1.3 71.5 - - - +
524A ARG* 1.3 57.8 + - - +
526A LEU* 2.7 23.9 + - - +
527A ALA* 2.9 11.6 + - - +
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Residues in contact with ARG 524 (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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507A GLU* 3.9 35.3 + - + +
508A ARG* 4.4 21.6 - - - +
520A GLU* 2.9 41.2 + - - +
521A VAL* 3.3 8.3 + - + +
523A ALA* 1.3 73.8 - - - +
525A ASN* 1.3 59.0 + - - +
526A LEU 2.7 15.1 + - - -
527A ALA* 3.0 10.4 + - - +
528A ARG* 3.0 49.4 + - + +
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Residues in contact with ASN 525 (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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521A VAL* 2.9 31.2 + - - +
522A LEU* 4.0 7.2 - - - +
524A ARG* 1.3 79.8 - - - +
526A LEU* 1.3 58.2 + - - +
528A ARG* 4.5 16.3 + - - +
529A ARG* 3.8 11.8 + - - +
547A VAL* 3.2 25.1 - - + +
548A GLU* 2.6 58.7 + - - +
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Residues in contact with LEU 526 (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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506A LEU* 4.9 0.2 - - - +
510A LEU* 4.1 10.1 - - + -
515A LEU* 5.6 3.4 - - + -
518A VAL* 3.8 20.4 - - + -
522A LEU* 3.3 30.4 + - + +
523A ALA* 2.7 14.7 + - - +
525A ASN* 1.3 81.0 - - - +
527A ALA* 1.3 60.1 + - - -
528A ARG 3.4 0.4 - - - -
529A ARG 3.4 0.7 + - - -
530A PHE* 3.0 42.2 + - + +
536A LEU* 4.8 16.5 - - + +
544A LEU* 4.8 6.7 - - + -
547A VAL* 3.9 27.1 - - + -
550A VAL* 4.1 7.6 - - + -
558A ILE* 4.0 19.1 - - + -
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Residues in contact with ALA 527 (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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506A LEU* 3.4 29.2 - - + -
507A GLU* 3.3 45.8 - - + +
510A LEU* 3.9 1.7 - - + +
523A ALA 2.9 5.2 + - - +
524A ARG 3.0 1.3 + - - +
526A LEU* 1.3 75.0 - - - +
528A ARG* 1.3 59.7 + - - +
531A GLY 2.7 31.5 + - - -
583A SER* 3.1 9.6 + - - +
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Residues in contact with ARG 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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507A GLU* 5.2 7.2 + - - +
524A ARG* 3.0 46.2 + - + +
525A ASN* 4.8 14.1 + - - +
527A ALA* 1.3 77.7 - - - +
529A ARG* 1.3 61.2 + - + +
530A PHE 3.4 1.0 + - - -
531A GLY* 4.1 3.3 + - - -
583A SER* 4.3 5.8 + - - -
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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