Contacts of the helix formed by residues 688 - 701 (chain A) in PDB entry 5M64
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 THR 688 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A PHE* 1.3 75.0 - - - +
689A ARG* 1.3 68.4 + - - +
690A GLU* 3.6 24.0 + - + +
691A GLN* 3.3 19.7 + - + +
692A TYR* 2.9 24.4 + - - +
723A TYR* 6.0 2.0 - - - -
724A PRO* 4.9 9.9 + - - +
725A LEU* 5.8 0.9 - - - -
726A TRP* 3.2 14.5 - - - -
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Residues in contact with ARG 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A THR* 1.3 82.3 + - - +
690A GLU* 1.3 75.4 + - - +
692A TYR* 3.7 3.7 - - + +
693A GLN* 3.1 60.3 + - + +
724A PRO* 5.5 5.6 + - + +
726A TRP* 3.5 21.1 - - + +
79H TRP* 4.3 29.0 - - + -
81H PRO* 5.4 12.6 - - - +
77K ARG* 5.0 0.8 - - - +
81K MET* 4.2 21.2 + - - +
83K ASN 5.9 0.2 + - - -
86K VAL* 2.6 31.7 + - - +
87K GLU* 3.3 11.5 + - - +
88K PHE 4.1 0.4 - - - +
108K TYR* 5.1 2.2 + - - -
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Residues in contact with GLU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A THR* 3.2 15.4 - - + +
689A ARG* 1.3 92.6 + - - +
691A GLN* 1.3 67.0 + - - +
694A GLN* 2.9 32.7 + - - +
77K ARG* 2.7 45.9 + - + +
78K TYR* 5.3 3.4 - - + -
81K MET* 3.2 46.4 - - + +
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Residues in contact with GLN 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A PHE* 3.6 28.9 - - + -
688A THR* 3.3 22.2 + - + +
690A GLU* 1.3 84.3 - - - +
692A TYR* 1.3 60.8 + - - +
694A GLN* 4.9 3.6 + - - +
695A TYR* 2.9 72.2 + - + +
731A ILE* 4.9 1.3 - - - -
823A ALA* 4.9 6.3 - - - +
1018B THR* 5.7 6.1 - - - +
1020B GLU* 4.7 12.7 + - - -
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Residues in contact with TYR 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A PHE* 4.9 0.4 - - - +
688A THR 2.9 17.4 + - - +
689A ARG* 3.7 5.8 - - + +
690A GLU 3.3 0.2 - - - -
691A GLN* 1.3 76.2 - - - +
693A GLN* 1.3 68.2 + - + +
696A ILE* 3.3 29.8 - - + +
714A THR* 3.7 23.6 - - + -
715A LEU* 3.2 21.8 + - - +
726A TRP* 3.4 59.9 - + + -
730A GLN* 4.0 9.6 - - + -
731A ILE* 3.6 23.1 - - + -
734A THR* 3.1 42.8 + - + -
88K PHE* 5.6 1.6 - + - -
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Residues in contact with GLN 693 (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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689A ARG* 3.1 58.3 + - + +
690A GLU 4.0 2.5 - - - +
692A TYR* 1.3 86.5 - - + +
694A GLN* 1.3 60.9 + - - +
695A TYR 3.3 0.4 - - - -
696A ILE* 3.4 1.0 - - - +
697A TYR* 3.0 25.5 + - - +
714A THR* 5.5 1.8 - - + +
77K ARG* 3.2 19.2 + - - +
87K GLU 3.2 15.0 + - - -
88K PHE* 3.3 37.6 - - + +
89K CYS 3.1 29.6 + - - +
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Residues in contact with GLN 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A GLU 2.9 17.3 + - - +
691A GLN* 4.6 4.3 + - - +
693A GLN* 1.3 74.9 - - - +
695A TYR* 1.3 80.7 + - - +
697A TYR 4.6 0.2 - - - +
698A GLY* 3.0 28.8 + - - +
819A ASN* 5.1 17.0 + - - +
823A ALA* 5.9 1.0 - - - +
77K ARG* 5.0 11.2 - - + +
90K GLY* 4.9 7.2 - - - -
91K TYR* 3.1 63.6 + - + +
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Residues in contact with TYR 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU* 4.9 2.5 - - + -
687A PHE* 4.5 19.9 - + - -
691A GLN* 2.9 60.6 + - + +
694A GLN* 1.3 92.2 - - - +
696A ILE* 1.3 58.3 + - - +
698A GLY* 4.6 0.2 - - - -
699A CYS* 3.1 28.2 + - - -
731A ILE* 4.6 17.7 - - + -
816A LEU* 3.7 19.1 - - + +
819A ASN* 4.4 8.2 + - + -
820A TYR* 3.4 56.1 + + + -
823A ALA* 3.3 25.3 - - + +
824A THR* 4.2 3.8 - - - +
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Residues in contact with ILE 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 3.3 25.8 + - + +
693A GLN 3.4 4.7 - - - +
695A TYR* 1.3 78.9 - - - +
697A TYR* 1.3 61.7 + - - +
699A CYS* 3.5 3.0 + - - +
700A ILE* 3.0 35.2 + - + +
712A ILE* 4.0 17.3 - - + -
713A VAL 5.4 1.3 - - - +
714A THR* 6.2 0.4 - - + -
731A ILE* 4.0 23.3 - - + +
734A THR* 3.7 28.0 - - + +
735A VAL* 4.8 12.3 - - + -
738A ASN* 4.3 16.4 - - - +
816A LEU* 5.3 2.0 - - + -
88K PHE* 3.5 28.0 - - + -
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Residues in contact with TYR 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A GLN 3.0 17.3 + - - +
694A GLN* 4.6 1.6 - - - +
696A ILE* 1.3 75.5 - - - +
698A GLY* 1.3 57.6 + - - +
699A CYS 3.0 10.7 + - - -
700A ILE* 4.3 2.9 - - - +
701A ARG* 3.1 29.4 + - + +
702A PRO* 3.5 31.0 - - + -
703A GLU* 5.1 3.5 - - - +
712A ILE* 5.8 2.2 - - + -
62K SER* 6.1 0.2 - - - -
88K PHE* 3.7 21.1 - + + -
90K GLY* 3.1 30.7 - - - -
91K TYR* 3.2 31.9 - - - -
92K SER* 3.2 21.1 + - - -
102K ASN* 3.2 14.3 + - - +
103K ILE 3.8 1.2 - - - -
104K ARG* 3.4 33.5 + - + +
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Residues in contact with GLY 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A GLN* 3.0 21.5 + - - -
697A TYR* 1.3 77.5 - - - +
699A CYS* 1.3 56.0 + - - +
701A ARG* 4.2 17.5 + - - -
815A ARG* 5.1 2.4 + - - +
819A ASN* 2.9 26.3 + - - +
91K TYR 4.1 12.3 - - - -
92K SER* 4.5 8.0 - - - -
93K ILE 5.5 0.7 + - - -
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Residues in contact with CYS 699 (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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695A TYR 3.1 23.1 - - - +
696A ILE* 3.5 3.9 + - - +
697A TYR 3.0 0.6 - - - -
698A GLY* 1.3 78.3 - - - +
700A ILE* 1.3 57.0 + - + +
701A ARG* 4.9 0.4 - - - -
735A VAL* 5.6 2.5 - - + -
812A VAL* 3.2 27.9 - - + +
815A ARG* 2.4 67.1 + - + +
816A LEU* 3.5 20.0 - - + -
819A ASN* 3.2 11.9 - - - -
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Residues in contact with ILE 700 (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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696A ILE* 3.0 23.9 + - + +
697A TYR* 3.3 2.4 + - + +
699A CYS* 1.3 75.3 - - - +
701A ARG* 1.3 63.0 + - - +
702A PRO* 3.7 16.2 - - + -
706A HIS* 2.4 62.2 + - + +
712A ILE* 3.6 33.0 - - + -
735A VAL* 3.7 33.2 - - + +
738A ASN* 5.0 4.5 - - + -
739A VAL* 5.0 5.2 - - + -
812A VAL* 4.0 16.6 - - + -
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Residues in contact with ARG 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ASN* 3.0 34.3 + - - +
697A TYR* 3.1 20.2 + - - +
698A GLY 4.2 14.1 + - - -
699A CYS 4.9 2.0 - - - -
700A ILE* 1.3 84.3 - - - +
702A PRO* 1.3 65.1 - - - +
703A GLU* 2.9 38.3 + - + -
704A ASP* 3.1 37.9 + - - +
705A GLY 3.4 4.0 + - - -
706A HIS* 3.7 1.8 + - - +
815A ARG* 4.2 9.9 - - - +
92K SER* 3.8 20.4 + - - +
93K ILE 2.5 32.0 + - - +
94K PRO* 3.3 15.1 + - - +
102K ASN* 4.0 6.3 - - - +
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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