Contacts of the strand formed by residues 795 - 802 (chain A) in PDB entry 1IU1
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 ARG 795 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A ALA* 3.3 4.3 - - - +
753A ALA* 2.9 41.8 + - + +
794A MET* 1.3 73.5 - - - +
796A ILE* 1.3 63.0 + - - +
810A LEU* 4.7 17.7 - - + -
811A ALA 3.4 7.4 - - - +
812A GLU* 3.2 34.2 + - + +
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Residues in contact with ILE 796 (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 ALA* 5.1 5.4 - - + +
710A TYR* 4.2 31.2 - - + -
717A ILE* 4.5 3.4 - - + -
719A PHE* 4.6 1.6 - - + -
750A PHE* 3.7 35.7 - - + -
751A GLN 3.3 7.9 - - - +
752A ALA* 4.3 0.4 - - + -
794A MET* 4.1 10.3 - - - -
795A ARG* 1.3 78.7 - - - +
797A LYS* 1.3 60.2 + - - +
798A LEU* 4.2 14.8 - - + -
809A ASP 3.9 0.5 - - - +
810A LEU* 3.3 7.0 - - - +
811A ALA* 2.7 50.9 + - + +
813A VAL* 3.8 26.2 - - + -
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Residues in contact with LYS 797 (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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749A VAL 3.6 2.9 - - - +
751A GLN* 2.9 65.3 + - + +
796A ILE* 1.3 74.1 - - - +
798A LEU* 1.3 68.2 + - - +
799A THR* 4.0 12.9 - - + +
808A GLN* 3.1 41.2 + - - +
809A ASP 3.3 8.3 - - - +
810A LEU* 4.2 14.9 - - + +
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Residues in contact with LEU 798 (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 TYR* 3.6 40.6 - - + +
715A LEU* 3.8 8.1 - - + -
717A ILE* 3.6 34.1 - - + -
748A PHE* 4.3 9.9 - - + -
749A VAL 3.5 2.5 - - - +
750A PHE* 3.7 20.9 - - + -
796A ILE* 4.3 11.0 - - + -
797A LYS* 1.3 81.0 - - - +
799A THR* 1.3 66.2 + - - +
800A TYR* 4.6 13.9 - - + -
808A GLN* 3.1 6.2 - - - +
809A ASP* 2.9 37.4 + - + +
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Residues in contact with THR 799 (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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747A ASP 3.5 2.3 + - - +
748A PHE* 3.4 0.9 - - - -
749A VAL* 2.8 53.0 + - - +
751A GLN* 4.9 5.0 + - - +
797A LYS* 4.0 29.8 - - + +
798A LEU* 1.3 79.7 - - - +
800A TYR* 1.3 68.1 + - - +
807A MET 3.3 11.7 - - - +
808A GLN* 4.2 7.0 - - + +
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Residues in contact with TYR 800 (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 TYR* 5.2 4.2 + - - -
712A LYS 4.6 0.7 + - - -
713A ASN* 4.2 16.1 + - - +
715A LEU* 3.7 29.0 - - + +
745A MET* 3.7 33.5 - - + +
746A THR 3.4 13.9 - - - +
747A ASP* 3.8 4.7 - - - -
748A PHE* 3.8 28.0 - + + -
798A LEU* 4.6 7.9 - - + -
799A THR* 1.3 84.1 - - - +
801A ASN* 1.3 58.5 + - - +
802A HIS* 3.7 19.0 + + + -
806A ALA* 3.7 1.8 - - - -
807A MET* 2.7 76.5 + - + +
808A GLN* 5.4 1.6 - - - -
809A ASP* 6.2 1.3 - - + -
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Residues in contact with ASN 801 (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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744A ASP 3.8 1.4 - - - +
745A MET* 3.4 3.6 - - - -
746A THR* 2.8 44.5 + - - +
747A ASP* 2.8 32.7 + - - +
800A TYR* 1.3 73.1 - - - +
802A HIS* 1.3 65.4 + - - +
804A GLY 6.2 0.7 - - - +
805A SER 3.3 12.5 - - - +
806A ALA* 3.6 16.3 + - - +
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Residues in contact with HIS 802 (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 ASN* 4.3 7.3 + - - +
741A THR* 3.0 41.6 + - + -
743A LEU* 3.3 21.0 + - + +
744A ASP 3.4 12.3 - - - -
745A MET* 3.6 19.2 - - + +
800A TYR* 3.7 21.1 + - + -
801A ASN* 1.3 76.2 - - - +
803A LYS* 1.3 104.2 + - + +
804A GLY 3.1 2.4 - - - +
805A SER* 2.9 30.8 + - - +
807A MET* 4.0 11.8 - - + +
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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