Contacts of the helix formed by residues 506 - 511 (chain B) in PDB entry 3GJN
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 ASP 506 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479B ARG* 3.5 35.8 + - - +
480B ILE* 3.7 13.4 - - + +
483B LYS* 5.4 3.0 + - + +
502B GLU 3.1 14.4 + - - +
503B VAL 3.4 4.1 + - - +
504B SER 3.5 0.4 - - - -
505B LYS* 1.3 77.6 - - - +
507B PRO* 1.4 74.1 - - - +
508B GLU* 2.6 40.0 + - - +
509B LEU* 2.7 32.9 + - + +
510B SER* 2.8 14.0 + - - -
515C ARG* 4.3 6.3 - - + -
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Residues in contact with PRO 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B ARG* 5.4 2.9 - - - +
505B LYS 3.3 10.2 - - - +
506B ASP* 1.4 85.6 - - - +
508B GLU* 1.3 79.3 + - + +
510B SER* 4.2 1.8 - - - +
511B LYS* 3.4 12.5 + - - +
510C SER 3.9 5.4 - - - +
511C LYS* 3.3 39.4 - - - +
513C PHE 3.4 24.2 - - - +
514C SER* 4.6 4.7 - - - -
515C ARG* 3.8 11.4 - - + +
518C ASN* 4.1 0.2 - - - -
1062D ASP* 6.0 0.2 - - - +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B ASN* 5.2 0.4 - - + -
479B ARG* 3.0 44.2 - - - +
506B ASP* 2.6 12.8 + - - +
507B PRO* 1.3 94.3 - - + +
509B LEU* 1.3 61.2 + - - +
511B LYS* 2.8 42.9 + - - +
512B GLN* 3.1 21.3 + - - -
511C LYS* 4.1 10.0 - - - +
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Residues in contact with LEU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B VAL* 3.5 31.6 - - + -
464B TRP* 3.9 20.0 - - + -
477B PRO* 3.6 13.2 - - + -
479B ARG* 5.0 5.4 - - - +
480B ILE* 3.2 43.1 - - + -
503B VAL* 3.6 24.5 - - + +
506B ASP* 2.7 14.4 + - + +
508B GLU* 1.3 83.4 - - + +
510B SER* 1.3 67.9 + - - +
511B LYS 3.1 0.9 - - - -
512B GLN* 2.7 25.7 + - - +
513B PHE* 3.6 11.5 - - - -
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Residues in contact with SER 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B VAL 3.4 3.4 + - - -
504B SER 3.1 30.8 + - - -
505B LYS 4.8 0.7 - - - -
506B ASP 2.8 17.1 + - - -
507B PRO* 3.8 4.5 + - - +
509B LEU* 1.3 78.6 - - - +
511B LYS* 1.3 62.6 + - - +
512B GLN 2.9 1.4 + - - -
513B PHE* 3.3 18.5 + - - +
518B ASN* 3.5 23.3 + - - +
507C PRO* 3.9 2.3 - - - +
510C SER* 2.8 30.3 + - - -
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Residues in contact with LYS 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B ASN* 3.5 37.3 + - - +
507B PRO 3.4 12.3 + - - +
508B GLU* 2.8 41.6 + - - +
509B LEU 2.9 0.6 + - - -
510B SER* 1.3 80.2 + - - +
512B GLN* 1.3 63.5 + - + +
507C PRO* 3.4 40.8 + - - +
508C GLU* 4.4 6.7 - - - +
511C LYS* 3.6 25.1 - - + +
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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