Contacts of the strand formed by residues 75 - 79 (chain C) in PDB entry 3DM6
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 LYS 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLU 4.8 4.4 + - - -
3A VAL 3.5 15.1 + - - -
4A ASP* 4.9 4.7 - - - -
48A VAL* 3.4 26.4 + - + +
68C TYR* 3.1 35.9 - - + +
69C VAL 3.4 15.3 - - - +
70C PRO* 3.7 9.9 - - + -
71C TYR* 4.5 2.2 - - - -
74C GLY* 1.3 77.0 - - - +
76C TRP* 1.3 61.3 + - - +
105C SER* 3.4 4.7 - - - -
106C ASP* 2.7 56.7 + - + +
108C PHE* 3.7 4.6 - - - +
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Residues in contact with TRP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.9 6.3 - - - -
37C ASN* 4.6 7.4 - - + -
39C ALA* 3.5 26.2 - - + -
67C VAL* 4.1 16.2 - - + -
68C TYR* 3.7 4.4 - - - -
69C VAL* 2.9 61.8 + - + +
71C TYR* 3.0 30.1 + + - -
75C LYS* 1.3 74.1 - - - +
77C GLU* 1.3 68.8 + - - +
78C GLY 4.2 2.5 - - - -
100C ALA* 3.7 22.2 - - + -
102C ILE* 3.5 28.7 - - + -
104C GLU 3.4 14.8 - - - +
105C SER* 3.7 12.1 - - - +
108C PHE* 3.6 37.2 - + + -
118C ILE* 4.6 0.2 - - - +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.1 4.7 - - - +
47A PHE* 4.1 4.2 - - - +
48A VAL* 3.1 27.8 + - + +
180A ASP* 2.8 26.1 - - - +
182A SER* 3.1 26.4 + - - +
67C VAL 3.1 10.1 - - - +
68C TYR* 4.1 5.8 - - + -
76C TRP* 1.3 80.2 - - - +
78C GLY* 1.3 59.8 + - - +
102C ILE* 3.7 2.9 - - - -
103C THR* 3.1 19.3 + - - +
104C GLU* 3.1 46.5 + - + +
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A SER* 4.8 1.3 - - - -
66C GLY* 3.6 2.4 - - - -
67C VAL* 2.8 39.4 + - - +
76C TRP* 4.0 3.9 - - - -
77C GLU* 1.3 75.5 - - - +
79C GLU* 1.3 65.1 + - - -
101C ALA 2.9 18.4 - - - -
102C ILE* 4.3 0.2 - - - -
103C THR* 3.7 10.1 - - - -
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ARG* 2.9 45.5 + - - +
60C TYR* 5.4 0.9 - - - +
62C ASP* 5.5 2.2 - - - +
65C LYS 3.3 14.6 - - - +
66C GLY* 5.3 2.0 - - - -
67C VAL* 4.5 0.2 - - - -
78C GLY* 1.3 74.3 - - - -
80C LEU* 1.3 66.5 + - - +
99C ILE 3.8 0.3 - - - +
100C ALA* 4.4 1.1 - - - -
101C ALA* 2.7 37.9 + - - +
103C THR* 3.5 20.5 + - - +
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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