Contacts of the strand formed by residues 712 - 721 (chain A) in PDB entry 3POZ
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 PHE 712 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707A LEU* 3.9 21.5 - - + -
708A LYS 3.4 22.0 - - - -
709A GLU* 3.1 26.5 - - + +
710A THR 3.4 1.7 + - - -
711A GLU* 1.3 80.6 + - - +
713A LYS* 1.3 70.1 + - - +
714A LYS* 4.4 8.3 - - - -
730A LEU 3.2 12.1 - - - +
731A TRP* 4.2 6.7 - - + -
732A ILE* 4.5 0.4 - - - +
742A VAL* 5.4 0.4 - - + -
744A ILE* 3.7 29.6 - - + -
781A CYS* 3.6 36.6 - - + -
787A GLN* 3.5 32.8 - - - -
789A ILE* 4.4 9.9 - - + -
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Residues in contact with LYS 713 (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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710A THR 5.6 4.3 - - - +
712A PHE* 1.3 81.3 - - - +
714A LYS* 1.3 63.7 + - - +
715A ILE* 4.1 18.4 - - + +
729A GLY* 3.0 6.4 - - - -
730A LEU* 2.9 36.7 + - + +
732A ILE* 3.8 28.1 - - + +
744A ILE* 3.7 4.3 - - - +
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Residues in contact with LYS 714 (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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709A GLU* 5.7 1.6 + - - -
712A PHE* 4.4 7.5 - - + -
713A LYS* 1.3 74.4 - - - +
715A ILE* 1.3 65.4 + - - +
727A TYR* 3.6 55.9 - - + -
728A LYS 3.9 3.8 - - - -
744A ILE* 4.0 14.8 - - + -
746A GLU* 4.1 10.3 + - - -
787A GLN* 2.8 36.1 + - - +
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Residues in contact with ILE 715 (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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713A LYS* 4.1 19.5 - - + +
714A LYS* 1.3 80.4 - - - +
716A LYS* 1.3 88.8 + - + +
728A LYS* 2.8 32.5 + - - +
729A GLY* 3.8 20.2 - - - -
730A LEU* 4.3 18.6 - - + +
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Residues in contact with LYS 716 (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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715A ILE* 1.3 98.1 - - + +
717A VAL* 1.3 65.2 + - - +
727A TYR* 3.2 11.5 - - - +
728A LYS* 2.8 58.1 + - + -
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Residues in contact with VAL 717 (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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716A LYS* 1.3 79.6 - - - +
718A LEU* 1.3 68.2 + - - +
719A GLY* 3.8 13.5 - - - +
720A SER* 4.9 4.3 - - - -
725A THR* 3.8 24.9 - - + -
726A VAL 3.9 2.2 - - - -
727A TYR* 3.8 22.7 - - + -
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Residues in contact with LEU 718 (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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716A LYS 3.7 0.8 + - - -
717A VAL* 1.3 78.4 - - - +
719A GLY* 1.3 57.3 + - - +
726A VAL* 2.8 24.1 + - + +
727A TYR 3.9 6.7 - - - +
728A LYS* 3.7 34.8 - - + +
743A ALA* 4.3 0.7 - - + -
792A LEU* 3.8 25.6 - - + -
997A PHE* 5.5 4.3 - - + -
1001A LEU* 4.2 27.8 - - + -
1023A 03P 3.9 33.0 - - + -
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Residues in contact with GLY 719 (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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717A VAL* 3.8 4.9 - - - -
718A LEU* 1.3 81.9 - - - +
720A SER* 1.3 60.8 + - - -
725A THR* 3.3 8.5 - - - +
726A VAL* 2.9 30.1 + - - +
1023A 03P 4.5 16.8 - - - -
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Residues in contact with SER 720 (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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717A VAL* 4.9 4.5 - - - -
719A GLY* 1.3 75.0 - - - -
721A GLY* 1.3 63.0 + - - +
724A GLY 3.6 7.7 + - - -
725A THR* 2.9 25.3 + - - -
1023A 03P 5.9 1.7 - - - +
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Residues in contact with GLY 721 (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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720A SER* 1.3 81.4 + - - +
722A ALA* 1.3 63.2 + - - -
724A GLY* 3.1 18.5 + - - +
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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