Contacts of the strand formed by residues 956 - 961 (chain D) in PDB entry 5NSS
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 956 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954D ASN 3.3 4.8 + - - -
955D LYS* 1.3 74.8 - - - +
957D SER* 1.3 63.9 + - - -
958D ILE* 3.5 1.4 + - - +
984D LEU* 5.4 2.8 - - - +
985D ILE 3.2 15.9 - - - -
986D ASP* 4.4 2.9 - - - -
987D GLU 5.4 0.2 - - - -
1010D GLN* 3.3 9.7 - - - +
1011D VAL* 2.9 32.1 + - - +
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Residues in contact with SER 957 (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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956D GLY* 1.3 70.5 - - - -
958D ILE* 1.3 62.4 + - - +
959D LYS* 3.7 5.7 + - - +
983D LYS 3.8 0.2 - - - +
984D LEU* 4.5 0.2 - - - -
985D ILE* 2.9 40.5 + - - +
1008D GLY* 5.7 4.7 - - - -
1009D GLU 3.5 16.4 - - - -
1010D GLN* 4.3 0.9 - - - +
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Residues in contact with ILE 958 (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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952D VAL* 5.9 1.8 - - + -
956D GLY 3.5 5.6 + - - +
957D SER* 1.3 72.0 - - - +
959D LYS* 1.3 59.5 + - - +
982D LEU* 6.4 1.3 - - + -
983D LYS 3.0 14.1 - - - +
984D LEU* 4.2 5.6 - - + +
1005D LYS 5.6 0.2 - - - +
1006D GLY 3.6 15.9 - - - +
1007D ASP* 4.0 9.4 - - - +
1008D GLY 4.8 1.9 + - - -
1009D GLU 4.0 6.6 + - - +
1010D GLN* 5.0 1.3 - - - +
1011D VAL* 4.9 13.5 - - + -
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Residues in contact with LYS 959 (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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957D SER* 3.7 5.7 + - - +
958D ILE* 1.3 75.4 - - - +
960D LEU* 1.3 63.6 + - - +
961D SER 4.0 1.3 + - - -
981D GLU 3.7 0.2 - - - +
982D LEU* 3.4 3.0 - - - -
983D LYS* 2.9 35.3 + - + +
1006D GLY 4.8 3.8 - - - -
1007D ASP* 5.1 6.7 - - + -
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Residues in contact with LEU 960 (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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959D LYS* 1.3 73.6 - - - +
961D SER* 1.3 62.5 + - - +
962D ASN 3.9 1.2 + - - -
963D VAL* 4.1 23.6 + - + +
965D SER* 6.4 2.0 - - - -
980D THR* 5.5 1.3 - - - -
981D GLU 2.7 15.3 - - - +
982D LEU* 5.1 2.2 - - + -
997D VAL* 5.9 1.8 - - + -
1006D GLY 5.1 6.3 + - - +
1007D ASP* 5.6 2.2 - - - +
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Residues in contact with SER 961 (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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959D LYS 4.0 2.4 + - - -
960D LEU* 1.3 70.5 - - - +
962D ASN* 1.3 68.5 + - - +
981D GLU* 2.9 46.9 + - - +
983D LYS* 6.0 5.2 - - - -
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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