Contacts of the strand formed by residues 919 - 922 (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 MET 919 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASP* 3.6 23.8 - - - +
133A GLY 4.2 4.0 - - - +
134A HIS* 3.3 36.1 - - + -
832D ILE* 3.7 31.0 - - + +
833D ALA 4.3 1.6 - - - +
834D TYR* 3.6 33.2 - - - +
835D THR* 3.6 26.5 - - + +
900D TYR 3.5 0.5 - - - +
901D ASP* 3.4 4.7 - - - -
902D ILE* 2.7 40.4 + - + +
917D ASN* 4.3 8.5 - - - +
918D VAL* 1.3 75.0 - - - +
920D ILE* 1.3 63.3 + - - +
921D CYS 4.1 0.4 - - - -
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Residues in contact with ILE 920 (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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88A LYS* 5.1 0.2 - - - -
90A GLU* 3.9 14.4 - - - +
126A THR* 4.1 8.1 - - - +
127A GLU* 3.3 38.8 - - + +
134A HIS* 3.6 32.1 + - + +
835D THR* 4.4 3.7 + - - -
869D THR* 3.8 17.7 - - + +
899D SER* 3.3 25.6 - - - +
900D TYR 3.2 2.0 - - - -
901D ASP* 4.1 12.3 - - - +
918D VAL 5.0 0.2 - - - +
919D MET* 1.3 78.0 - - - +
921D CYS* 1.3 62.5 + - - +
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Residues in contact with CYS 921 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835D THR* 3.3 42.4 - - - +
836D GLU* 4.0 7.6 - - - -
837D ALA 4.0 6.7 - - - -
843D ILE* 3.7 22.9 - - + +
899D SER* 3.5 2.6 - - - -
900D TYR* 2.8 37.9 + - - +
902D ILE* 3.9 17.7 - - + -
919D MET 4.1 0.4 - - - -
920D ILE* 1.3 75.2 - - - +
922D GLU* 1.3 65.4 + - - +
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Residues in contact with GLU 922 (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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45A TYR* 5.6 1.6 + - - -
178A SER* 2.7 35.0 + - - -
179A ARG* 4.7 3.3 + - - +
180A ASN* 3.9 14.8 + - - +
181A HIS* 5.1 2.6 + - - -
837D ALA* 3.4 17.0 - - - +
843D ILE* 4.4 1.1 - - - -
897D GLU* 4.4 13.2 - - - +
898D THR 3.3 16.4 - - - +
899D SER* 4.1 8.4 + - - +
921D CYS* 1.3 77.9 - - - +
923D THR* 1.3 76.8 + - - +
924D LYS* 5.3 0.2 - - - +
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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