Contacts of the helix formed by residues 519 - 528 (chain A) in PDB entry 2IN6
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 ASN 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A PRO* 3.5 11.5 - - - +
518A ARG* 1.3 88.6 + - - +
520A GLY* 1.3 68.6 + - - +
521A ASP 4.0 0.3 + - - -
522A GLN* 4.8 0.9 + - - +
523A TRP* 3.2 19.4 + - - +
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Residues in contact with GLY 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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519A ASN* 1.3 84.1 - - - +
521A ASP* 1.3 64.1 + - - -
523A TRP* 3.3 15.3 - - - +
524A HIS* 3.3 19.7 + - - -
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Residues in contact with ASP 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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520A GLY* 1.3 69.5 - - - -
522A GLN* 1.3 63.7 + - + +
523A TRP 3.2 1.6 - - - -
524A HIS* 3.4 10.7 + - - +
525A GLU* 3.1 25.3 + - - +
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Residues in contact with GLN 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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515A PRO 5.2 2.9 - - - +
517A PRO* 3.6 32.1 - - + +
519A ASN 5.1 0.7 - - - +
521A ASP* 1.3 78.1 - - - +
523A TRP* 1.3 61.9 + - - +
525A GLU* 3.5 6.5 + - - +
526A ILE* 3.4 28.9 + - + +
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Residues in contact with TRP 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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480A SER* 2.9 29.8 + - - -
483A LEU* 3.7 26.0 - - + -
485A ASN* 3.8 18.2 - - - -
488A LEU* 3.6 28.5 - - + -
517A PRO* 3.3 29.0 - - + +
518A ARG 3.5 11.9 - - - -
519A ASN* 3.2 25.5 + - - +
520A GLY 3.3 5.5 + - - +
521A ASP 3.2 0.4 - - - -
522A GLN* 1.3 81.1 - - - +
524A HIS* 1.3 94.6 + + - +
526A ILE 3.5 0.2 + - - -
527A ARG* 3.2 64.5 + - + +
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Residues in contact with HIS 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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485A ASN* 5.0 7.7 + - - -
488A LEU* 5.7 3.1 - - + -
520A GLY* 3.3 30.3 + - - -
521A ASP* 3.4 10.7 + - - +
522A GLN 3.4 0.4 - - - -
523A TRP* 1.3 101.2 - + - +
525A GLU* 1.3 60.2 + - - +
527A ARG* 3.3 6.7 + - - +
528A GLN* 3.0 38.2 + - + +
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Residues in contact with GLU 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 ASP 3.1 17.4 + - - +
522A GLN* 3.8 8.3 - - - +
523A TRP 3.4 0.2 - - - -
524A HIS* 1.3 72.1 - - - +
526A ILE* 1.3 66.1 + - + +
528A GLN* 3.2 24.1 + - - +
530A ARG* 3.4 39.2 + - + +
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Residues in contact with ILE 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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501A PHE* 4.4 4.3 - - + -
505A LEU* 4.0 29.8 - - + -
516A LEU* 4.5 4.5 - - + -
517A PRO* 3.6 29.6 - - + -
522A GLN* 3.4 18.9 + - + +
523A TRP 3.8 4.9 - - - +
524A HIS 3.3 0.4 - - - -
525A GLU* 1.3 77.5 - - + +
527A ARG* 1.3 73.0 + - - +
529A GLY* 2.7 27.2 + - - -
530A ARG 3.4 19.7 + - - +
532A PRO* 4.0 23.6 - - + -
550A ILE* 3.9 10.7 - - + +
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Residues in contact with ARG 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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481A ARG 3.4 23.8 + - - -
483A LEU 2.7 41.9 + - - +
485A ASN* 3.5 37.3 - - + +
501A PHE* 3.2 32.2 - - + -
505A LEU* 4.0 0.8 - - - +
517A PRO* 4.7 1.2 + - - +
523A TRP* 3.2 69.2 + - + +
524A HIS* 3.3 10.4 + - - +
526A ILE* 1.3 94.7 - - - +
528A GLN* 1.3 62.3 + - - +
529A GLY 3.1 5.9 + - - -
550A ILE 4.7 0.5 - - - +
552A PRO* 3.4 22.5 - - - +
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Residues in contact with GLN 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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524A HIS* 3.0 25.0 + - + +
525A GLU* 3.3 20.2 - - - +
526A ILE 3.1 0.6 - - - -
527A ARG* 1.3 78.3 - - - +
529A GLY* 1.3 57.0 + - - +
530A ARG* 3.6 11.7 - - + +
552A PRO* 3.8 21.4 - - - +
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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