Contacts of the strand formed by residues 831 - 837 (chain D) in PDB entry 3N1Q
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 HIS 831 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLU 5.4 4.5 - - - -
132A ASP 4.8 3.9 + - - -
830D PRO* 1.3 77.3 - - - +
832D ILE* 1.3 76.4 + - - +
833D ALA* 3.4 8.4 + - + -
847D TRP* 4.0 2.5 - - - -
848D THR* 2.8 50.1 + - - +
917D ASN* 3.2 28.2 + - + +
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Residues in contact with ILE 832 (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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132A ASP 4.6 1.2 - - - +
831D HIS* 1.3 77.6 + - - +
833D ALA* 1.3 65.8 + - - +
834D TYR 3.7 16.8 - - - +
835D THR* 3.8 6.3 - - + -
845D LEU* 4.3 18.8 - - + -
846D LYS 3.7 11.7 - - - +
847D TRP* 3.9 2.7 - - + -
902D ILE* 3.6 28.3 - - + +
903D LYS* 4.3 0.9 - - - -
904D MET* 4.0 21.1 - - + -
916D SER* 3.6 17.3 - - - +
917D ASN* 3.1 36.6 + - - +
919D MET* 3.7 23.5 - - + +
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Residues in contact with ALA 833 (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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132A ASP 5.6 0.5 - - - +
133A GLY 4.6 7.1 - - - +
831D HIS* 3.4 13.2 + - + +
832D ILE* 1.3 74.1 - - - +
834D TYR* 1.3 70.7 + - + +
846D LYS* 2.7 35.6 + - + +
847D TRP* 4.9 0.7 - - - -
848D THR* 4.9 8.3 - - + -
919D MET* 4.3 4.4 - - - +
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Residues in contact with TYR 834 (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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133A GLY 5.7 0.7 - - - +
834C TYR* 2.8 28.2 + + - -
844C MET* 3.0 24.9 - - + +
846C LYS* 3.9 24.0 - - + +
888C TRP* 3.3 31.7 - + + -
832D ILE* 3.5 1.9 - - - +
833D ALA* 1.3 90.4 - - + +
835D THR* 1.3 70.6 + - - +
836D GLU* 4.1 18.8 - - + -
844D MET* 4.9 4.5 - - + -
846D LYS* 3.1 48.7 + - + +
919D MET* 3.6 10.3 - - - -
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Residues in contact with THR 835 (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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134A HIS* 4.9 1.4 - - - +
832D ILE* 3.8 7.0 - - + -
834D TYR* 1.3 81.9 - - - +
836D GLU* 1.3 68.0 + - - +
843D ILE* 4.5 0.2 - - - -
844D MET 3.1 7.4 - - - -
845D LEU* 3.7 20.4 - - + -
902D ILE* 4.2 13.7 - - + -
919D MET* 3.6 36.7 - - + +
920D ILE 4.4 3.3 + - - -
921D CYS* 3.3 32.6 - - - +
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Residues in contact with GLU 836 (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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886C LYS* 3.4 35.7 - - - +
887C GLN* 4.5 3.3 + - - +
888C TRP* 3.0 55.2 + - + +
834D TYR* 4.1 17.9 - - + -
835D THR* 1.3 80.3 - - - +
837D ALA* 1.3 64.2 + - - +
838D VAL* 3.9 0.7 - - - +
844D MET* 2.8 35.9 + - + +
921D CYS* 4.0 4.7 - - - -
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Residues in contact with ALA 837 (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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888C TRP* 3.8 12.5 - - - -
836D GLU* 1.3 75.3 + - - +
838D VAL* 1.3 59.3 + - - +
839D SER 4.1 0.2 - - - +
842D GLN 3.7 12.8 - - - +
843D ILE* 4.2 5.2 - - + +
921D CYS* 4.0 4.9 - - - -
922D GLU 3.4 25.8 - - - +
923D THR* 4.1 6.1 - - - -
924D LYS* 3.4 33.8 + - + -
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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