Contacts of the strand formed by residues 941 - 947 (chain A) in PDB entry 3I7L
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 941 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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903A CYS* 3.2 24.9 - - - +
935A TYR* 3.3 15.0 - - - -
936A LYS* 2.6 45.4 + - - +
939A GLU* 3.8 26.7 - - + +
940A GLY* 1.3 77.7 + - - +
942A PHE* 1.3 86.6 - - - +
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Residues in contact with PHE 942 (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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903A CYS* 3.9 16.9 - - + -
904A ASN 3.6 22.9 - - - -
905A HIS* 3.6 43.3 - + + +
906A TYR 5.0 0.7 - - - -
933A LEU* 3.8 14.4 - - + -
934A ALA 3.5 6.5 - - - -
935A TYR* 4.8 1.8 - - + +
936A LYS* 4.8 1.6 - - - -
941A ASN* 1.3 101.6 - - - +
943A GLU* 1.3 63.2 + - - +
944A GLU* 4.8 4.5 - - + -
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Residues in contact with GLU 943 (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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933A LEU* 3.2 3.2 - - - +
934A ALA* 3.0 33.4 + - + +
936A LYS* 3.2 41.9 + - + +
942A PHE* 1.3 74.7 - - - +
944A GLU* 1.3 67.3 + - - +
945A ILE* 3.2 22.4 + - + +
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Residues in contact with GLU 944 (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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905A HIS* 3.1 24.0 + - + +
907A ASN* 2.7 33.8 + - - +
931A LEU* 4.2 14.7 - - + +
932A LEU 3.9 12.6 - - - +
933A LEU* 4.2 5.5 - - + +
942A PHE* 4.2 6.5 + - + -
943A GLU* 1.3 73.9 - - - +
945A ILE* 1.3 64.7 + - - +
946A ALA 4.3 4.6 - - - +
947A ARG* 4.1 23.6 + - - +
990A GLN* 3.7 16.7 + - - +
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Residues in contact with ILE 945 (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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921A ILE* 5.0 6.5 - - + -
932A LEU* 3.2 21.1 + - + +
933A LEU 4.9 0.2 - - - -
934A ALA* 4.2 22.7 - - + +
943A GLU* 3.2 27.1 + - + +
944A GLU* 1.3 76.2 - - - +
946A ALA* 1.3 69.0 + - + +
979A LYS* 4.1 28.0 - - - +
989A ARG* 3.7 15.7 - - + +
990A GLN* 3.5 13.5 + - - -
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Residues in contact with ALA 946 (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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931A LEU* 3.9 3.1 - - - +
932A LEU* 3.2 30.8 + - + +
944A GLU* 3.8 6.4 - - - +
945A ILE* 1.3 86.4 - - + +
947A ARG* 1.3 65.6 + - - +
979A LYS* 5.1 6.1 - - + -
989A ARG 4.0 7.0 - - - +
990A GLN* 3.1 22.0 - - - +
991A HIS 4.5 1.6 - - - +
992A LEU* 3.8 23.6 - - + -
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Residues in contact with ARG 947 (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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907A ASN* 4.1 13.6 + - - +
925A ASP* 3.9 7.0 - - - -
928A ARG* 3.1 56.1 - - - +
930A VAL 3.3 23.1 - - - -
931A LEU* 4.2 8.1 - - + +
944A GLU* 4.1 19.4 + - - +
946A ALA* 1.3 79.4 - - - +
948A ASP* 1.3 70.5 + - - +
949A PHE* 3.5 52.4 - - + +
990A GLN 3.1 5.2 + - - +
991A HIS* 3.6 0.2 - - - -
992A LEU* 3.0 26.9 + - - +
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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