Contacts of the strand formed by residues 721 - 729 (chain H) in PDB entry 1N3E
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 721 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716H PHE 3.7 0.4 + - - -
717H VAL* 2.8 34.2 + - - +
720H ASP* 1.3 81.8 - - - +
722H SER* 1.3 65.4 + - - -
744H GLN 3.2 13.5 - - - -
745H VAL* 4.2 5.8 - - - +
798H LYS* 3.1 16.8 + - - -
965L G 3.5 8.8 - - - +
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Residues in contact with SER 722 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717H VAL* 4.4 3.2 - - - +
721H GLY* 1.3 75.2 - - - -
723H ILE* 1.3 63.0 + - - +
724H ILE* 3.1 20.5 - - - +
742H THR 3.5 3.5 - - - +
743H PHE* 3.6 2.3 - - - -
744H GLN* 2.9 53.3 + - - +
798H LYS* 4.8 1.8 - - - -
965L G 3.7 12.8 - - - +
966L A 2.7 28.6 + - - -
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Residues in contact with ILE 723 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717H VAL* 4.9 7.9 - - + -
722H SER* 1.3 75.1 + - - +
724H ILE* 1.3 60.2 + - - +
742H THR 3.7 3.6 - - - +
743H PHE* 4.3 17.3 - - + -
788H LEU* 4.1 18.6 - - + -
795H LEU* 4.2 7.9 - - + -
798H LYS* 3.7 22.5 - - + +
801H GLN* 3.7 24.6 - - + +
802H ALA* 3.6 28.3 - - + +
805H VAL* 3.7 28.3 - - + -
832H ILE* 3.8 5.9 - - - +
836H ASN* 2.9 25.1 + - - +
966L A 4.2 2.0 + - - -
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Residues in contact with ILE 724 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722H SER* 3.1 28.3 - - - +
723H ILE* 1.3 74.4 - - - +
725H ALA* 1.3 65.6 + - - +
726H GLN* 3.9 18.2 - - + +
740H SER 4.0 0.3 - - - +
741H LEU* 3.4 5.2 - - - +
742H THR* 2.8 53.7 + - + +
744H GLN* 3.7 20.2 - - + +
805H VAL* 4.7 3.7 - - - +
832H ILE* 4.8 0.7 - - - -
836H ASN* 4.6 2.0 - - - +
966L A 3.6 26.5 - - + +
967L C 3.4 40.8 - - + +
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Residues in contact with ALA 725 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724H ILE* 1.3 77.6 - - - +
726H GLN* 1.3 64.0 + - - +
740H SER 3.4 4.9 - - - -
741H LEU* 3.8 16.8 - - + -
808H ILE* 4.4 1.1 - - + -
829H VAL* 3.5 31.8 - - + +
832H ILE* 3.7 36.4 - - + +
833H ALA* 5.5 1.7 - - - +
841H ARG* 5.0 3.1 + - - -
967L C 4.5 9.1 + - - +
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Residues in contact with GLN 726 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724H ILE* 3.9 12.5 - - + +
725H ALA* 1.3 77.7 - - - +
727H ILE* 1.3 64.5 + - - +
728H LYS* 3.7 33.4 + - + +
738H GLN 3.6 1.0 - - - +
739H LEU* 3.7 4.9 - - - +
740H SER* 2.9 38.4 + - - +
742H THR* 4.8 8.7 + - - +
829H VAL* 4.5 2.7 - - - -
841H ARG* 5.9 1.1 - - - +
967L C 3.4 31.1 + - - +
968L G 2.7 57.2 + - - +
969L T 4.7 0.8 - - - +
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Residues in contact with ILE 727 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726H GLN* 1.3 75.0 - - - +
728H LYS* 1.3 60.0 + - - +
729H PRO* 3.5 0.7 - - - +
737H HIS* 3.7 18.8 - - + -
738H GLN 3.7 3.4 - - - +
739H LEU* 4.2 7.4 - - + -
822H PHE* 4.9 0.4 - - + -
826H CYS* 3.6 35.9 - - + +
829H VAL* 3.8 27.8 - - + +
841H ARG* 4.1 0.7 - - - +
843H THR* 3.0 39.3 + - + +
844H THR 3.7 26.7 - - - +
845H SER* 3.8 2.0 - - - +
848H VAL* 3.4 24.7 - - + -
968L G 4.7 3.7 + - - -
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Residues in contact with LYS 728 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726H GLN* 3.7 34.7 + - + -
727H ILE* 1.3 74.6 - - - +
729H PRO* 1.3 70.3 - - + +
730H ASN* 3.6 2.1 + - + +
737H HIS* 3.1 3.0 - - - -
738H GLN* 2.6 60.7 + - + +
740H SER* 3.4 28.3 + - - -
742H THR* 5.8 0.4 + - - -
904I A 5.9 1.0 + - - -
905I A 3.9 15.5 + - - +
906I A 4.0 5.1 - - - +
968L G 4.6 1.2 + - - +
969L T 3.1 44.1 + - + +
970L T 4.8 9.9 - - + +
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Residues in contact with PRO 729 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727H ILE 3.5 9.2 - - - +
728H LYS* 1.3 83.2 - - + +
730H ASN* 1.3 65.5 + - - +
736H LYS 4.4 0.4 - - - +
737H HIS* 3.3 23.3 - - + +
843H THR* 3.7 17.0 - - + +
969L T 4.0 22.4 - - + +
970L T 4.8 14.5 - - + +
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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