Contacts of the helix formed by residues 700 - 707 (chain A) in PDB entry 2MYS
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 VAL 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A MET* 5.8 0.7 - - + -
102A VAL* 4.6 8.3 - - + -
106A LEU* 6.2 1.1 - - + -
119A SER* 3.9 14.8 - - - +
122A PHE* 3.4 32.2 - - + -
124A VAL* 4.2 20.9 - - + -
673A ARG* 4.7 4.0 - - + -
695A LEU* 3.7 18.8 - - + +
698A ASN* 3.4 20.3 - - + +
699A GLY* 1.3 76.9 - - - +
701A LEU* 1.3 77.9 + - + +
703A GLY* 3.2 1.2 + - - -
704A ILE* 3.2 26.3 + - + +
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Residues in contact with LEU 701 (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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98A HIS 5.2 2.0 - - - +
99A GLU* 3.6 37.2 - - + +
102A VAL* 4.4 17.7 - - + -
692A LEU* 4.6 2.5 - - + +
695A LEU* 3.0 44.0 + - + +
696A ARG* 4.0 20.4 - - + +
700A VAL* 1.3 93.9 - - + +
702A GLU* 1.3 60.3 + - - +
704A ILE* 3.9 11.1 - - + +
705A ARG* 3.2 42.3 + - - +
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Residues in contact with GLU 702 (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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488A GLN* 4.9 10.7 - - - +
491A PHE* 5.4 0.2 - - - -
492A ASN* 3.7 21.2 + - - -
518A ASP* 5.9 1.4 - - - +
519A LEU* 4.8 3.6 - - - +
584A TYR* 4.4 27.9 - - + +
696A ARG 5.4 4.8 + - - +
699A GLY* 2.9 16.4 + - - +
701A LEU* 1.3 78.3 - - - +
703A GLY* 1.3 63.9 + - - +
704A ILE 3.2 0.7 - - - -
705A ARG* 3.4 18.8 - - - +
706A ILE* 3.1 45.4 + - + +
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Residues in contact with GLY 703 (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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119A SER 5.7 1.1 - - - -
122A PHE* 4.8 3.6 - - - -
491A PHE* 4.3 20.4 - - - -
495A MET* 4.3 6.8 - - - +
699A GLY 2.8 14.2 + - - -
700A VAL 3.2 2.4 + - - -
702A GLU* 1.3 78.6 - - - +
704A ILE* 1.3 67.3 + - - +
706A ILE* 3.9 6.3 - - - +
707A CYS* 3.1 30.2 + - - +
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Residues in contact with ILE 704 (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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91A MET 5.8 1.1 - - - +
92A ALA* 4.8 14.6 - - + +
97A LEU* 4.2 38.6 - - + +
98A HIS 4.8 6.7 - - - +
102A VAL* 4.3 18.8 - - + -
119A SER* 3.1 36.8 - - - +
120A GLY* 5.7 0.2 - - - -
700A VAL* 3.2 15.6 + - + +
701A LEU* 3.9 13.5 - - + +
703A GLY* 1.3 78.8 - - - +
705A ARG* 1.3 62.5 + - - +
707A CYS* 3.0 7.3 + - + +
708A ARG* 2.9 35.2 + - - +
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Residues in contact with ARG 705 (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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99A GLU* 4.2 19.3 + - - -
696A ARG* 6.0 3.2 - - - +
701A LEU* 3.2 38.1 + - - +
702A GLU* 3.4 25.8 - - - +
704A ILE* 1.3 83.7 - - - +
706A ILE* 1.3 63.8 + - + +
708A ARG* 3.0 50.6 + - - +
709A LYS* 3.3 20.6 + - + +
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Residues in contact with ILE 706 (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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491A PHE* 5.0 2.0 - - + -
492A ASN* 4.1 25.6 - - + +
495A MET* 3.7 24.9 - - - -
499A GLU* 4.9 8.1 - - + +
515A PHE* 3.7 60.0 - - + -
702A GLU* 3.1 31.2 + - - +
703A GLY* 3.9 6.5 - - - +
705A ARG* 1.3 79.9 - - + +
707A CYS* 1.3 63.3 + - - +
709A LYS* 3.6 17.2 + - + +
710A GLY 4.0 5.2 + - - -
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Residues in contact with CYS 707 (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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92A ALA* 4.7 20.4 - - + +
97A LEU* 4.9 9.4 - - + -
120A GLY* 5.8 1.1 - - - -
495A MET* 4.0 22.2 - - - -
499A GLU* 5.2 9.3 - - - +
703A GLY 3.1 19.5 + - - +
704A ILE* 3.0 15.4 + - + +
705A ARG 2.9 0.8 - - - -
706A ILE* 1.3 74.0 - - - +
708A ARG* 1.3 58.5 + - - +
709A LYS 2.9 10.6 + - - -
710A GLY* 3.1 12.8 + - - -
711A PHE 4.2 0.5 + - - -
712A PRO* 3.5 24.7 - - + +
714A ARG* 5.2 3.7 + - - +
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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