Contacts of the strand formed by residues 69 - 75 (chain B) in PDB entry 4KMR
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 GLY 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B SER* 1.3 76.8 - - - +
70B VAL* 1.3 60.0 + - - -
98B ASP 3.1 9.3 + - - -
99B LEU* 3.3 18.5 - - - -
100B VAL* 2.9 27.7 + - - +
126B ASP* 3.5 11.0 - - - -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.0 21.5 - - + -
68B SER 4.1 7.9 - - - +
69B GLY* 1.3 79.4 - - - +
71B ILE* 1.3 63.7 + - - +
99B LEU* 4.2 1.2 - - - +
100B VAL* 3.5 18.6 - - + +
102B LEU* 3.9 32.3 - - + -
124B LEU 3.5 23.6 - - - +
125B THR* 4.0 2.9 - - - -
126B ASP* 2.7 45.2 + - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY 4.3 0.2 - - - -
70B VAL* 1.3 79.2 - - - +
72B GLY* 1.3 62.1 + - - +
90B VAL* 4.7 2.0 - - + -
94B ALA* 4.3 12.1 - - + -
99B LEU* 4.2 22.9 - - + -
100B VAL 2.9 16.0 + - - +
101B VAL* 3.3 25.2 - - + -
102B LEU* 2.9 23.2 + - - +
125B THR* 3.6 7.0 - - - +
127B GLY 3.4 8.1 - - - +
129B LEU* 3.9 28.0 - - + -
311B VAL* 4.4 9.2 - - + -
314B LEU* 3.6 23.8 - - + -
318B ILE* 4.0 17.3 - - + -
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 1.3 77.6 - - - +
73B LEU* 1.3 60.3 + - - +
101B VAL* 4.6 0.9 - - - -
102B LEU 3.3 9.0 - - - -
104B GLU* 5.5 2.0 - - - -
125B THR* 3.4 15.2 - - - +
127B GLY 2.9 12.9 + - - -
128B LEU* 3.6 13.0 - - - -
129B LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLY* 1.3 74.5 - - - +
74B ALA* 1.3 61.2 + - - +
75B VAL* 4.0 23.1 - - + -
86B LEU* 6.1 3.8 - - + -
87B ALA* 3.7 37.0 - - + +
90B VAL* 4.4 24.7 - - + -
91B ILE* 5.4 0.9 - - + -
101B VAL* 3.7 17.9 - - + +
102B LEU 2.9 6.2 + - - +
103B VAL* 3.4 17.4 - - + +
104B GLU* 2.9 28.7 + - - +
128B LEU* 4.1 0.4 - - - +
129B LEU* 3.4 24.5 - - + +
130B LEU 6.0 0.2 - - - -
131B ALA* 5.7 2.9 - - + +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLY 4.3 0.4 - - - -
73B LEU* 1.3 72.7 - - - +
75B VAL* 1.3 63.6 + - - +
104B GLU* 3.4 28.9 - - + +
106B THR* 4.3 9.4 - - + -
116B ALA* 4.4 3.1 - - + -
128B LEU* 4.3 7.4 - - + -
129B LEU 3.0 9.7 + - - +
130B LEU* 3.7 23.2 - - + +
131B ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 4.0 26.5 - - + -
74B ALA* 1.3 78.4 - - - +
76B PRO* 1.4 76.1 - - + +
77B GLU* 4.0 14.6 - - - +
78B LEU* 4.1 26.5 - - + +
83B PHE* 4.0 27.1 - - + +
86B LEU* 5.7 3.4 - - + -
87B ALA* 5.3 0.7 - - + +
103B VAL* 4.8 5.2 - - + -
104B GLU 3.1 9.8 + - - +
105B GLN* 3.1 7.0 - - + -
106B THR* 2.9 23.0 + - - -
131B ALA* 4.3 6.1 - - + -
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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