Contacts of the helix formed by residues 711 - 716 (chain D) in PDB entry 2JDQ
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 711 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709D SER* 3.2 8.0 + - - +
710D ILE* 1.3 92.5 + - - +
712D GLU* 1.3 59.1 + - + +
713D LEU 3.2 0.6 + - - -
714D SER* 3.0 25.1 + - - -
715D ASN* 5.5 0.5 - - - +
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Residues in contact with GLU 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707D ALA 5.0 0.3 - - - +
708D LEU* 3.2 37.3 - - + +
709D SER* 3.0 41.4 + - - +
711D ASN* 1.3 76.0 - - + +
713D LEU* 1.3 62.5 + - - +
714D SER 3.3 0.4 - - - -
715D ASN* 3.1 28.3 + - + +
716D LEU 3.9 2.4 + - - -
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Residues in contact with LEU 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690D VAL* 4.9 4.3 - - + -
691D LEU* 4.3 13.2 - - + -
694D PHE* 3.8 43.1 - - + -
708D LEU* 4.5 11.2 - - + -
709D SER 3.4 6.1 + - - +
710D ILE* 3.7 17.7 - - + +
711D ASN 3.2 1.4 - - - -
712D GLU* 1.3 74.9 - - - +
714D SER* 1.3 65.0 + - - +
716D LEU* 3.0 31.6 + - + +
722D ALA* 5.1 0.2 - - + -
724D VAL* 3.6 48.2 - - + -
734D VAL* 3.8 11.9 - - + -
736D LYS* 3.6 8.7 - - - -
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Residues in contact with SER 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690D VAL* 5.8 4.9 - - - +
694D PHE* 4.8 2.4 - - - -
710D ILE 4.8 1.0 + - - -
711D ASN 3.0 18.2 + - - -
713D LEU* 1.3 76.0 - - - +
715D ASN* 1.3 68.2 + - - +
736D LYS* 2.8 24.8 + - - +
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Residues in contact with ASN 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D GLU* 3.1 17.6 + - - +
713D LEU 3.1 1.2 - - - -
714D SER* 1.3 86.1 + - - +
716D LEU* 1.3 63.2 + - - +
717D ALA* 3.3 3.8 + - - -
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Residues in contact with LEU 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694D PHE* 4.4 10.5 - - + -
708D LEU* 4.7 8.1 - - + -
712D GLU 3.9 1.8 + - - -
713D LEU* 3.0 35.6 + - + +
714D SER 3.3 0.2 - - - -
715D ASN* 1.3 75.1 - - - +
717D ALA* 1.3 74.8 + - - +
718D LYS 3.4 0.3 + - - -
720D GLU* 3.9 35.4 - - + +
721D LYS 4.4 3.6 - - - +
722D ALA* 3.6 35.9 - - + +
734D VAL 4.3 6.7 - - - +
735D MET* 4.5 4.3 - - - -
736D LYS* 2.6 34.4 + - + +
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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