Contacts of the strand formed by residues 71 - 76 (chain A) in PDB entry 1M9H
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 PHE 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.7 10.3 - - + -
12A ASN* 5.5 0.9 - - + -
13A SER 3.0 28.9 - - - -
14A ILE* 3.7 29.8 - - + -
15A PRO* 3.6 29.3 - - + +
42A ARG 2.7 9.7 + - - +
43A HIS* 3.1 11.5 - + - -
44A ILE 2.7 34.0 + - - +
69A ASP 4.3 0.2 + - - -
70A LEU* 1.3 72.3 - - - +
72A ILE* 1.3 59.5 + - - +
73A THR* 3.4 24.2 - - - -
103A ASP* 3.4 28.9 - - + -
104A LEU* 3.6 21.1 - - + -
134A ARG* 4.3 7.4 - - - -
135A SER* 5.5 0.4 - - - -
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Residues in contact with ILE 72 (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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44A ILE* 3.7 25.1 - - + +
46A THR* 5.1 2.0 - - + -
56A VAL* 5.0 3.6 - - + -
60A ILE* 3.7 23.1 - - + -
67A ARG* 3.9 26.7 - - - +
70A LEU* 4.3 11.9 - - + -
71A PHE* 1.3 81.2 - - - +
73A THR* 1.3 67.7 + - - +
74A THR 4.3 0.2 - - - -
97A LEU* 4.4 15.7 - - + -
99A LEU* 4.0 22.4 - - + -
102A VAL* 3.8 12.2 - - + +
103A ASP* 2.8 38.8 + - - +
104A LEU 3.1 7.3 + - - +
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Residues in contact with THR 73 (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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43A HIS* 4.0 7.1 + - - -
44A ILE 3.0 11.6 + - - -
45A ASP* 3.5 25.1 + - - +
46A THR* 2.8 34.8 + - - +
71A PHE* 3.4 26.3 - - - -
72A ILE* 1.3 73.8 - - - +
74A THR* 1.3 71.5 + - - +
75A LYS* 4.8 1.3 - - - -
104A LEU* 3.4 22.5 - - + +
106A LEU* 4.1 20.4 - - + -
185A GLU* 4.7 0.6 + - - +
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Residues in contact with THR 74 (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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46A THR* 3.6 11.7 - - - -
47A ALA* 3.3 11.8 + - - -
48A ALA 3.4 0.9 + - - -
53A GLU* 2.5 30.1 + - - +
72A ILE 4.3 0.4 + - - -
73A THR* 1.3 76.5 - - - +
75A LYS* 1.3 73.4 + - - +
90A ILE* 5.6 0.2 - - + -
93A SER* 3.9 11.2 - - - -
97A LEU* 4.1 4.9 - - + -
102A VAL* 3.9 22.4 - - + +
104A LEU 3.3 5.5 + - - +
105A TYR* 3.3 27.2 - - + -
106A LEU 3.0 19.1 + - - -
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Residues in contact with LYS 75 (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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45A ASP* 2.8 29.5 + - - -
46A THR 2.9 19.3 + - - +
47A ALA* 3.8 5.1 - - + +
48A ALA* 3.6 22.7 + - - +
49A ILE 5.1 0.2 + - - -
50A TYR* 3.1 23.4 + - - -
73A THR* 4.9 0.2 - - + -
74A THR* 1.3 88.9 + - - +
76A LEU* 1.3 62.4 + - - +
77A TRP 3.6 2.6 + - - -
93A SER* 4.9 0.3 + - - -
105A TYR* 3.8 8.3 + - - -
106A LEU* 3.1 26.7 - - + +
108A HIS* 3.6 37.9 + - + +
139A SER* 5.1 0.7 - - - -
161A GLN* 3.3 32.0 + - - +
300A NAD 4.4 2.9 - - - +
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Residues in contact with LEU 76 (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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48A ALA* 5.8 0.2 - - - -
75A LYS* 1.3 65.3 - - - +
77A TRP* 1.3 67.1 + - - +
78A ASN* 4.5 0.2 - - - +
80A ARG* 3.6 29.8 - - + +
81A HIS* 4.2 15.1 + - + -
86A PRO* 4.0 22.4 - - + +
89A ALA* 3.5 31.9 - - + -
105A TYR* 3.5 19.8 - - + +
106A LEU 2.4 27.7 + - - +
107A VAL* 3.9 12.0 - - + -
108A HIS* 2.9 29.6 + - - +
109A TRP 4.6 0.3 + - - -
120A ALA* 4.6 5.8 - - + -
124A MET* 4.2 14.8 - - + -
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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