Contacts of the strand formed by residues 712 - 719 (chain A) in PDB entry 3RLN
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 712 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A ILE* 3.6 9.7 - - - +
676A ASN* 5.2 0.7 - - - -
708A GLN* 3.4 2.5 - - - +
709A ASP* 3.0 35.2 + - - +
710A ALA 3.4 1.0 + - - -
711A THR* 1.3 79.9 - - - +
713A LYS* 1.3 61.7 + - - -
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Residues in contact with LYS 713 (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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675A ILE* 3.5 8.3 - - - +
679A CYS* 4.4 8.5 - - - +
694A HIS* 5.2 10.2 + - + +
695A LYS* 5.9 1.8 - - - +
706A GLU* 3.5 38.2 + - + +
707A ILE 3.1 16.6 - - - +
708A GLN* 4.2 7.9 - - + -
712A GLY* 1.3 74.5 - - - +
714A MET* 1.3 65.8 + - - +
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Residues in contact with MET 714 (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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675A ILE* 3.5 22.7 - - + +
678A LEU* 3.7 38.1 - - + -
679A CYS* 4.1 8.1 - - + -
706A GLU* 3.3 8.5 - - - +
707A ILE* 2.9 46.8 + - + -
713A LYS* 1.3 75.3 - - - +
715A GLU* 1.3 67.5 + - - +
740A LEU* 4.4 2.5 - - + -
748A GLY 3.4 27.4 - - - +
749A GLU* 3.8 2.7 - - - -
750A LEU* 3.7 35.0 - - + +
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Residues in contact with GLU 715 (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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697A ASN* 5.9 0.9 - - - +
699A ARG* 4.4 7.6 + - - -
704A TYR* 3.5 41.6 - - + +
705A TYR 3.2 9.4 - - - +
706A GLU* 4.3 18.4 + - + +
714A MET* 1.3 85.3 - - - +
716A VAL* 1.3 63.6 + - - +
717A VAL* 4.1 0.7 - - + -
743A LYS* 5.4 3.6 + - - -
748A GLY 4.7 2.4 + - - -
749A GLU* 3.3 20.6 - - + +
750A LEU 3.0 23.7 + - - -
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Residues in contact with VAL 716 (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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703A THR 3.5 4.2 - - - +
704A TYR* 3.5 2.0 - - - -
705A TYR* 2.8 43.0 + - + +
707A ILE* 3.7 37.7 - - + -
715A GLU* 1.3 77.0 - - - +
717A VAL* 1.3 61.5 + - - +
718A VAL* 4.0 9.6 + - + -
733A LEU* 4.6 11.2 - - + -
735A LEU* 4.3 13.2 - - + -
738A PHE* 3.7 31.9 - - + -
750A LEU* 3.2 18.4 - - + +
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Residues in contact with VAL 717 (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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702A PHE* 3.9 23.8 - - + -
703A THR 3.6 2.9 - - - +
704A TYR* 3.4 45.1 - - + +
715A GLU* 4.8 0.9 - - + -
716A VAL* 1.3 75.1 - - - +
718A VAL* 1.3 65.3 + - - +
719A HIS* 5.1 0.7 + - - -
738A PHE* 4.4 0.5 - - - -
749A GLU* 3.2 36.6 - - + +
750A LEU 2.7 13.9 + - - +
751A ARG* 3.4 7.4 - - + +
752A SER* 2.9 28.6 + - - -
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Residues in contact with VAL 718 (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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701A GLU 3.9 0.2 - - - +
702A PHE* 3.2 9.8 - - - +
703A THR* 2.9 39.0 + - - +
705A TYR* 4.2 18.6 - - + -
716A VAL* 4.4 5.4 - - + -
717A VAL* 1.3 77.9 - - - +
719A HIS* 1.3 65.1 + - - +
722A LEU* 3.2 44.9 - - + +
723A THR* 3.6 7.5 - - + +
738A PHE* 4.1 14.1 - - + -
752A SER* 3.5 3.4 - - - +
758A ILE* 4.1 24.0 - - + -
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Residues in contact with HIS 719 (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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701A GLU* 3.6 6.3 - - + +
702A PHE* 3.7 29.8 - + + -
717A VAL 5.1 0.4 + - - -
718A VAL* 1.3 77.4 - - - +
720A GLY* 1.3 73.3 + - - +
721A ARG* 3.7 1.6 + - - +
722A LEU* 3.8 8.7 + - - +
723A THR* 3.6 8.7 - - - -
752A SER* 3.0 50.2 + - - -
753A VAL* 4.8 6.9 - - - -
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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