Contacts of the strand formed by residues 59 - 63 (chain A) in PDB entry 1MMG
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 SER 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.4 5.0 - - - +
56A THR* 2.9 35.4 + - - +
58A ASP* 1.3 89.1 - - - +
60A PHE* 1.3 56.8 + - - +
71A GLN* 2.3 33.5 + - - -
72A VAL 2.7 21.1 - - - -
73A LYS* 4.0 1.3 - - - -
74A LYS* 3.0 19.2 - - - +
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Residues in contact with PHE 60 (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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33A ARG* 3.5 28.9 - - - -
35A ILE* 5.4 1.3 - - + -
52A ILE* 4.1 32.3 - - + -
54A SER 3.6 0.9 - - - -
55A GLU* 3.9 10.8 - - + -
59A SER 1.3 72.5 - - - -
61A THR* 1.3 66.9 + - - +
62A PHE* 4.0 0.7 - - + -
71A GLN* 2.9 3.7 - - - +
72A VAL* 2.3 64.1 + - + +
74A LYS* 3.2 59.0 - - + -
77A ALA* 3.7 21.5 - - + -
79A GLN* 4.3 20.4 - - - -
753A ARG* 5.5 2.5 - - - -
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Residues in contact with THR 61 (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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52A ILE* 3.7 1.4 - - - -
53A VAL* 2.8 25.6 + - + +
54A SER* 2.6 38.6 + - - +
56A THR* 4.1 5.2 - - - +
59A SER* 4.1 0.5 + - - -
60A PHE* 1.3 77.0 - - - +
62A PHE* 1.3 59.7 + - - +
69A ASP* 5.5 6.1 - - + -
70A ARG 3.0 13.5 - - - +
71A GLN* 2.6 45.6 + - + -
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Residues in contact with PHE 62 (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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35A ILE* 3.7 24.9 - - + -
37A TYR* 3.4 40.4 - + + -
50A GLY* 4.2 0.2 - - - -
51A GLU 2.7 25.4 - - - +
52A ILE* 3.6 5.8 - - + -
53A VAL* 3.5 7.6 - - - -
60A PHE* 4.4 2.5 - - + -
61A THR* 1.3 77.0 - - - +
63A LYS* 1.3 69.9 + - - +
64A THR* 4.3 6.1 - - + -
69A ASP* 3.3 1.9 - - - +
70A ARG* 2.6 69.1 + - + -
71A GLN 4.4 0.9 - - - -
72A VAL* 2.9 38.4 - - + -
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Residues in contact with LYS 63 (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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50A GLY* 3.3 21.3 - - - -
51A GLU* 2.8 19.0 + - + +
53A VAL* 3.5 14.4 - - + +
62A PHE* 1.3 76.2 - - - +
64A THR* 1.3 68.7 + - - +
67A GLY* 4.8 8.5 - - - +
68A GLN 3.2 9.2 - - - +
69A ASP* 4.2 3.8 - - + +
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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