Contacts of the strand formed by residues 71 - 78 (chain A) in PDB entry 2DMH
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ILE 4.5 2.1 - - - +
35A PHE* 3.2 17.8 - - - -
69A SER 3.7 7.5 + - - -
70A SER* 1.3 77.9 - - - +
72A LEU* 1.3 60.9 + - - +
73A GLY 4.2 0.5 + - - -
92A THR* 4.0 20.5 - - - +
93A VAL 3.4 13.0 - - - -
94A ALA* 4.1 8.1 - - - -
95A LEU* 3.9 11.3 - - - +
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Residues in contact with LEU 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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9A LEU* 3.7 18.8 - - + -
11A VAL* 3.5 36.6 - - + -
33A VAL* 3.6 25.1 - - + -
34A ILE 4.2 0.9 - - - +
35A PHE* 3.6 26.0 - - + -
71A SER* 1.3 73.9 - - - +
73A GLY* 1.3 59.9 + - - +
74A ILE* 3.9 12.0 + - + -
92A THR* 3.4 9.7 - - - +
93A VAL* 2.8 45.1 + - + +
95A LEU* 4.1 6.5 - - + +
127A LEU* 5.9 0.7 - - + -
129A ILE* 3.8 17.9 - - + -
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Residues in contact with GLY 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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32A SER 3.1 14.6 - - - +
33A VAL* 3.4 3.8 - - - -
34A ILE* 3.4 32.1 + - - +
71A SER 4.2 0.4 + - - -
72A LEU* 1.3 73.6 - - - +
74A ILE* 1.3 62.6 + - - +
75A ILE* 4.0 7.0 - - - -
91A ALA 4.2 1.8 - - - -
92A THR* 4.9 5.8 - - - -
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Residues in contact with ILE 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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11A VAL* 5.0 0.9 - - + -
31A VAL* 4.4 14.8 - - + -
32A SER 3.8 0.7 - - - +
33A VAL* 3.5 34.3 - - + -
72A LEU* 4.1 8.7 - - + -
73A GLY* 1.3 82.4 - - - +
75A ILE* 1.3 62.6 + - - +
76A VAL* 4.5 12.8 - - + -
90A THR* 3.2 4.7 - - - -
91A ALA* 2.7 52.0 + - + +
93A VAL* 4.5 14.4 - - + -
111A ILE* 6.1 0.2 - - + -
113A LEU* 4.8 10.3 - - + -
125A ILE* 4.8 4.7 - - + -
127A LEU* 3.7 33.2 - - + -
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Residues in contact with ILE 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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30A ILE 3.5 1.9 - - - +
32A SER* 3.1 40.3 + - - +
34A ILE* 4.1 22.4 - - + -
39A LYS* 5.1 5.4 - - - +
73A GLY* 4.7 3.1 - - - +
74A ILE* 1.3 82.3 - - - +
76A VAL* 1.3 62.7 + - - +
77A LYS* 4.1 32.5 + - + +
87A LEU* 4.8 4.3 - - + -
89A GLY 3.9 0.9 - - - -
90A THR* 3.3 26.5 - - + -
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Residues in contact with VAL 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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19A ILE* 5.2 5.2 - - + -
29A PRO* 4.3 7.6 - - + -
30A ILE 3.5 23.8 - - - +
31A VAL* 4.5 8.7 - - + -
53A TRP* 5.3 3.6 - - + -
74A ILE* 4.3 15.9 - - + -
75A ILE* 1.3 76.1 - - - +
77A LYS* 1.3 67.2 + - - +
88A ILE* 3.2 24.1 + - + +
89A GLY 2.8 39.5 + - - +
113A LEU* 4.4 22.7 - - + -
125A ILE* 4.5 13.7 - - + -
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Residues in contact with LYS 77 (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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28A ASP 3.3 2.8 - - - +
29A PRO* 3.4 2.6 - - - +
30A ILE* 3.2 36.1 + - + +
32A SER* 5.0 12.1 + - - -
39A LYS* 6.0 2.0 - - - +
75A ILE* 4.1 27.1 + - + +
76A VAL* 1.3 80.1 - - - +
78A ASP* 1.3 63.6 + - - +
79A PHE 3.9 0.2 - - - -
81A THR 5.3 2.9 - - - +
86A LYS 3.9 19.7 - - - +
87A LEU* 4.1 18.6 - - + -
88A ILE* 3.4 13.9 - - - +
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Residues in contact with ASP 78 (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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27A PRO* 4.1 19.2 - - + +
28A ASP* 3.0 30.3 + - - +
30A ILE* 5.0 0.2 - - - -
77A LYS* 1.3 74.9 - - - +
79A PHE* 1.3 57.4 + - - +
80A GLU* 3.0 23.2 + - - +
81A THR* 2.6 68.6 + - - +
86A LYS* 4.2 19.3 + - + +
88A ILE* 3.6 8.9 - - + +
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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